hravs (v2.17.2) graph data
type: Ontology
creator: hra-do-processor
description: The graph representation of the HuBMAP Research Attributes Value Set dataset.
license: https://creativecommons.org/licenses/by/4.0/
publisher: HuBMAP
date created: 2026-06-08
version: v2.17.2
type: NamedIndividual
type: ConceptScheme
has top concept: Source storage duration unit
has top concept: Preparation medium
has top concept: Preparation condition
has top concept: Processing time unit
has top concept: Storage medium
has top concept: Storage method
has top concept: Thickness unit
has top concept: Area unit
has top concept: Volume unit
has top concept: Tissue weight unit
has top concept: Pathology distance unit
has top concept: Suspension entity type
has top concept: Dataset type
has top concept: Dataset type (SenNet)
has top concept: Analyte class
has top concept: Acquisition instrument vendor
has top concept: Acquisition instrument model
has top concept: Time since acquisition instrument calibration unit
has top concept: Stain name
has top concept: Stain technique
has top concept: Preparation instrument vendor
has top concept: Preparation instrument model
has top concept: Tile configuration
has top concept: Scan direction
has top concept: Total run time unit
has top concept: Laterality
has top concept: Organ condition
has top concept: Perfusion solution
has top concept: Transport solution
has top concept: Warm ischemic time unit
has top concept: Cold ischemic time unit
has top concept: Weight unit
has top concept: Height unit
has top concept: Width unit
has top concept: Length unit
has top concept: Library input amount unit
has top concept: Library output amount unit
has top concept: Library concentration unit
has top concept: Library layout
has top concept: Library preparation kit
has top concept: Sample indexing kit
has top concept: Barcode read
has top concept: UMI read
has top concept: Sequencing reagent kit
has top concept: Transposition reagent kit
has top concept: Transposition method
has top concept: Assay input unit
has top concept: Assay input entity
has top concept: Preparation instrument kit
has top concept: Amount of input analyte unit
has top concept: Mapped area unit
has top concept: Spot size unit
has top concept: Spot spacing unit
has top concept: Permeabilization time unit
has top concept: RNA probe panel
has top concept: MS ionization technique
has top concept: Mass analysis polarity
has top concept: Ion mobility
has top concept: MS scan mode
has top concept: Matrix deposition method
has top concept: Preparation matrix
has top concept: Desorption solvent
has top concept: Desorption solvent flow rate unit
has top concept: Data collection mode
has top concept: LC instrument vendor
has top concept: LC column vendor
has top concept: LC column length unit
has top concept: LC temperature unit
has top concept: LC inner diameter unit
has top concept: LC flow rate unit

Sample ID
type: AnnotationProperty
definition: Unique HuBMAP or SenNet identifier for the sample assigned by the ingest portal.
preferred label: sample_id

Source storage duration value
type: AnnotationProperty
definition: How long was the source material (parent) stored, prior to this sample being processed? For tissue blocks, this would typically be the time between when the organ arrived in the lab and the processing of the organ began. In most cases this will likely be 0, while in some cases the organ might be stored (on ice) in the lab before dissection. For tissue sections, this would be how long the tissue block was stored, usually in a -80 freezer, prior to the section being cut. For suspensions, this would be the length of time the tissue block was stored prior to the initiation of the dissociation process.
preferred label: source_storage_duration_value

Source storage duration unit
type: AnnotationProperty
definition: Time unit.
preferred label: source_storage_duration_unit

Preparation medium
type: AnnotationProperty
definition: The media used during preparation of the sample.
preferred label: preparation_medium

Preparation condition
type: AnnotationProperty
definition: The condition under which the preparation occurred, such as whether the sample was placed in dry ice during the preparation.
preferred label: preparation_condition

Processing time value
type: AnnotationProperty
definition: How long was the tissue being handled before the initial preservation? For tissue blocks, this would typically be the length of time from when the organ was received in the lab to when the tissue block is frozen or otherwise preserved (e.g., embedded in OCT). For a tissue section this would be how long it takes to slice the tissue block and fix the mounted slice, after removing the tissue block from the freezer. For a suspension this would be the length of time from when the tissue block is removed from the freezer, dissociated and processed to the point where by the suspension is put into the initial preservation buffer.
preferred label: processing_time_value

Processing time unit
type: AnnotationProperty
definition: Time unit
preferred label: processing_time_unit

Storage medium
type: AnnotationProperty
definition: The medium in which the sample is stabilized for storage.
preferred label: storage_medium

Storage method
type: AnnotationProperty
definition: The method by which the sample was stored, after preparation and before the assay was performed.
preferred label: storage_method

Quality criteria
type: AnnotationProperty
definition: For suspensions, measured by visual inspection prior to cell lysis or defined by known parameters such as wells with several cells or no cells. This can be captured at a high level. "OK" or "not OK", or with more specificity such as "debris", "clump", "low clump".
preferred label: quality_criteria

Histological report
type: AnnotationProperty
definition: Histopathological reporting of key variables that are important for the tissue (absence of necrosis, comment on composition, significant pathology description, high level inflammation/fibrosis assessment, etc.)
preferred label: histological_report

Thickness value
type: AnnotationProperty
definition: Thickness of a tissue section
preferred label: thickness_value

Thickness unit
type: AnnotationProperty
definition: Thickness unit
preferred label: thickness_unit

Section index number
type: AnnotationProperty
definition: The index number for the section if the sample is a single section.
preferred label: section_index_number

Area value
type: AnnotationProperty
definition: The area of a tissue section.
preferred label: area_value

Area unit
type: AnnotationProperty
definition: Area unit
preferred label: area_unit

Notes
type: AnnotationProperty
definition: Miscellaneous details about the sample, not captured in the existing metadata fields.
preferred label: notes

Metadata schema ID
type: AnnotationProperty
definition: The ID that uniquely identifies the version of the metadata schema being used.
preferred label: metadata_schema_id

Volume value
type: AnnotationProperty
definition: The volume of an entity
preferred label: volume_value

Volume unit
type: AnnotationProperty
definition: The unit of measurment for volume.
preferred label: volume_unit

Tissue weight value
type: AnnotationProperty
definition: Weight of a tissue block or the piece of tissue.
preferred label: tissue_weight_value

Tissue weight unit
type: AnnotationProperty
definition: The unit of measurement for tissue weight.
preferred label: tissue_weight_unit

Pathology distance value
type: AnnotationProperty
definition: If surgical sample, how far from the pathology was the sample obtained. Typically a number of centimeters. Leave blank if not applicable or unknown.
preferred label: pathology_distance_value

Pathology distance unit
type: AnnotationProperty
definition: Distance unit.
preferred label: pathology_distance_unit

Suspension entity type
type: AnnotationProperty
definition: The type of single cell entity derived from isolation protocol.
preferred label: suspension_entity_type

Suspension entity count
type: AnnotationProperty
definition: Total number of cell/nuclei yielded post dissociation and enrichment.
preferred label: suspension_entity_count

Is suspension enriched?
type: AnnotationProperty
definition: Was the cell/nuclei population enriched?
preferred label: is_suspension_enriched

Suspension enriched target
type: AnnotationProperty
definition: If the suspension was enriched, then this is the target of the enrichment.
preferred label: suspension_enriched_target

Lab ID
type: AnnotationProperty
definition: An internal field labs can use it to add whatever ID(s) they want or need for dataset validation and tracking. This could be a single ID (e.g., "Visium_9OLC_A4_S1") or a delimited list of IDs (e.g., “9OL; 9OLC.A2; Visium_9OLC_A4_S1”). This field will not be accessible to anyone outside of the consortium and no effort will be made to check if IDs provided by one data provider are also used by another.
preferred label: lab_id

Dataset type
type: AnnotationProperty
definition: The specific main type of assay being executed.
preferred label: dataset_type

Analyte class
type: AnnotationProperty
definition: Analytes are the target molecules being measured with the assay.
preferred label: analyte_class

Is targeted?
type: AnnotationProperty
definition: Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. The CODEX analyte is protein.
preferred label: is_targeted

Acquisition instrument vendor
type: AnnotationProperty
definition: An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.
preferred label: acquisition_instrument_vendor

Acquisition instrument model
type: AnnotationProperty
definition: Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.
preferred label: acquisition_instrument_model

Time since acquisition instrument calibration value
type: AnnotationProperty
definition: The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture.
preferred label: time_since_acquisition_instrument_calibration_value

Time since acquisition instrument calibration unit
type: AnnotationProperty
definition: The time since acquisition instrument calibration units
preferred label: time_since_acquisition_instrument_calibration_unit

Contributors path
type: AnnotationProperty
definition: The path to the file with the ORCID IDs for all contributors of this dataset. This is an internal metadata field that is just used for ingest.
preferred label: contributors_path

Data path
type: AnnotationProperty
definition: The top level directory containing the raw and/or processed data. For a single dataset upload this might be "." where as for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For instance, if the data is within a directory called "TEST001-RK" use syntax "./TEST001-RK/" for this field. If there are multiple directory levels, use the format "./TEST001-RK/Run1/Pass2" in which "Pass2" is the subdirectory where the single dataset's data is stored. This is an internal metadata field that is just used for ingest.
preferred label: data_path

Is image preprocessing required?
type: AnnotationProperty
definition: Depending on if the acquisition instrument was a microscope, slide scanner, etc. will indicate whether or not any level of preprocessing was required to assemble the image (e.g., fusing image tiles).
preferred label: is_image_preprocessing_required

Stain name
type: AnnotationProperty
definition: The name of the chemical stains (dyes) applied to histology samples to highlight important features of the tissue as well as to enhance the tissue contrast.
preferred label: stain_name

Stain technique
type: AnnotationProperty
definition: There are typically three types of stains: progressive, modified progressive, and regressive. Progressive staining occurs when the hematoxylin is added to the tissue without being followed by a differentiator to remove excess dye. With regressive and modified progressive staining, a differentiator is used.
preferred label: stain_technique

Is batch staining done?
type: AnnotationProperty
definition: Were the slides stained using a linear batch method or individually?
preferred label: is_batch_staining_done

Is staining automated?
type: AnnotationProperty
definition: Was the slide staining automated with an instrument?
preferred label: is_staining_automated

Preparation instrument vendor
type: AnnotationProperty
definition: The manufacturer of the instrument used to prepare (staining/processing) the sample for the assay. If an automatic slide staining method was indicated this field should list the manufacturer of the instrument.
preferred label: preparation_instrument_vendor

Preparation instrument model
type: AnnotationProperty
definition: Manufacturers of a staining system instrument may offer various versions (models) of that instrument with different features. Differences in features or sensitivities may be relevant to processing or interpretation of the data.
preferred label: preparation_instrument_model

Slide ID
type: AnnotationProperty
definition: A unique ID denoting the slide used. This allows users the ability to determine which tissue sections were processed together on the same slide. It is recommended that data providers prefix the ID with the center name, to prevent values overlapping across centers. For Visium this should be the slide serial number provided by 10X
preferred label: slide_id

Tile configuration
type: AnnotationProperty
definition: This is how the tiles are configured for stitching.
preferred label: tile_configuration

Scan direction
type: AnnotationProperty
definition: This is the direction of imaging, which is required for stitching.
preferred label: scan_direction

Tiled image columns
type: AnnotationProperty
definition: This is how many columns used in stitching. This is sometimes referred to as the grid size x.
preferred label: tiled_image_columns

Tiled image count
type: AnnotationProperty
definition: This is the total number of raw (tiled) images captured, that are to be stitched together.
preferred label: tiled_image_count

Intended tile overlap percentage
type: AnnotationProperty
definition: The amount of overlap between tiled images. This is the set point, where as during image acquisition there will be slight variations due to stage registration.
preferred label: intended_tile_overlap_percentage

Number of antibodies
type: AnnotationProperty
definition: Number of antibodies
preferred label: number_of_antibodies

Number of channels
type: AnnotationProperty
definition: The number of distinct color channels in the image.
preferred label: number_of_channels

Number of biomarker imaging rounds
type: AnnotationProperty
definition: Number of imaging rounds to capture the tagged biomarkers. For CODEX a biomarker imaging round consists of 1. oligo application, 2. fluor application, 3. washes. For Cell DIVE a biomarker imaging round consists of 1. staining of a biomarker via secondary detection or direct conjugate and 2. dye inactivation.
preferred label: number_of_biomarker_imaging_rounds

Number of total imaging rounds
type: AnnotationProperty
definition: The total number of acquisitions performed on microscope to collect autofluorescence/background or stained signal (e.g., histology).
preferred label: number_of_total_imaging_rounds

Total run time value
type: AnnotationProperty
definition: How long the tissue was on the acquisition instrument.
preferred label: total_run_time_value

Total run time unit
type: AnnotationProperty
definition: The time unit of the total run time.
preferred label: total_run_time_unit

Organ ID
type: AnnotationProperty
definition: Unique HuBMAP or SenNet identifier for the organ.
preferred label: organ_id

Laterality
type: AnnotationProperty
definition: Which side of the body did the organ come from. This would be "Not applicable" for blood, where as an organ like the uterus would be midline.
preferred label: laterality

Organ condition
type: AnnotationProperty
definition: Health status of the organ at the time of sample recovery.
preferred label: organ_condition

Perfusion solution
type: AnnotationProperty
definition: Type of solution that was used to perfuse the organ.
preferred label: perfusion_solution

Transport solution
type: AnnotationProperty
definition: Type of solution used during transport.
preferred label: transport_solution

Warm ischemic time value
type: AnnotationProperty
definition: Time interval from interruption of blood supply of tissue to cooling to 4 degrees Celsius. For organ donor: cessation of blood flow to perfusion of organ (cooled to 4 degrees Celsius). For surgical specimen/biopsy: cessation of blood flow to specimen (time biopsy taken or blood supply is interrupted) to cooling of specimen to 4 degrees Celsius.
preferred label: warm_ischemic_time_value

Warm ischemic time unit
type: AnnotationProperty
definition: The unit of measurement for warm ischemic time.
preferred label: warm_ischemic_time_unit

Cold ischemic time value
type: AnnotationProperty
definition: Time interval from cooling to 4 degrees Celsius to final preservation. For organ donor: organ preservation flush (cooled to 4 degrees Celsius) to final preservation (freezing or fixation). For surgical specimen/biopsy: time specimen is placed at 4 degrees Celsius to final preservation (freezing or fixation).
preferred label: cold_ischemic_time_value

Cold ischemic time unit
type: AnnotationProperty
definition: The unit of measurement for cold ischemic time.
preferred label: cold_ischemic_time_unit

Pathology report
type: AnnotationProperty
definition: General pathologist report. Further details on organ level QC checks.
preferred label: pathology_report

Weight value
type: AnnotationProperty
definition: The weight of an entity.
preferred label: weight_value

Weight unit
type: AnnotationProperty
definition: The unit of measurement of weight.
preferred label: weight_unit

Height value
type: AnnotationProperty
definition: The height of an entity.
preferred label: height_value

Height unit
type: AnnotationProperty
definition: The unit of measurement of height.
preferred label: height_unit

Width value
type: AnnotationProperty
definition: The width of an entity.
preferred label: width_value

Width unit
type: AnnotationProperty
definition: The unit of measurement of width.
preferred label: width_unit

Length value
type: AnnotationProperty
definition: The length of an entity.
preferred label: length_value

Length unit
type: AnnotationProperty
definition: The unit of measurement of length.
preferred label: length_unit

Source ID
type: AnnotationProperty
definition: Unique HuBMAP or SenNet identifier for the source (parent) from which the sample was taken.
preferred label: source_id

Preparation protocol DOI
type: AnnotationProperty
definition: The protocol used when procuring or preparing the block, section or suspension. This must be provided as a DOI URL.
preferred label: preparation_protocol_doi

Parent sample ID
type: AnnotationProperty
definition: Unique HuBMAP or SenNet identifier of the sample (i.e., block, section or suspension) used to perform this assay. For example, for a RNAseq assay, the parent would be the suspension, whereas, for one of the imaging assays, the parent would be the tissue section. If an assay comes from multiple parent samples then this should be a comma separated list
preferred label: parent_sample_id

Library adapter sequence
type: AnnotationProperty
definition: 5’ and/or 3’ read adapter sequences used as part of the library preparation protocol to render the library compatible with the sequencing protocol and instrumentation. This should be provided as comma-separated list of key:value pairs (adapter name:sequence).
preferred label: library_adapter_sequence

Library average fragment size
type: AnnotationProperty
definition: Average size of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation. Numeric value in base pairs (bp).
preferred label: library_average_fragment_size

Library input amount value
type: AnnotationProperty
definition: The amount of cDNA, after amplification, that was used for library construction.
preferred label: library_input_amount_value

Library input amount unit
type: AnnotationProperty
definition: Unit of library input amount value.
preferred label: library_input_amount_unit

Library output amount value
type: AnnotationProperty
definition: Calculate the total library yield following the clean-up step of the final PCR amplification. To find this, simply multiply the Qubit-measured concentration (ng/µl) by the elution volume (µl) after the final clean-up.
preferred label: library_output_amount_value

Library output amount unit
type: AnnotationProperty
definition: Units of library output amount
preferred label: library_output_amount_unit

Library concentration value
type: AnnotationProperty
definition: The concentration value of the pooled library samples submitted for sequencing.
preferred label: library_concentration_value

Library concentration unit
type: AnnotationProperty
definition: Unit of library concentration value.
preferred label: library_concentration_unit

Library layout
type: AnnotationProperty
definition: Whether the library was generated for single-end or paired end sequencing.
preferred label: library_layout

Number of library PCR cycles
type: AnnotationProperty
definition: Number of PCR cycles performed in order to add adapters and amplify the library. Usually, this includes 5 pre-amplificationn cycles followed by 0-5 additional cycles determined by qPCR or number of PCR cycles to amplify cDNA.
preferred label: number_of_library_pcr_cycles

Number of PCR cycles for indexing
type: AnnotationProperty
definition: Number of PCR cycles performed in order to add adapters and amplify the library. This does not include the cDNA amplification which is captured in the "number of iterations of cDNA amplification" field.
preferred label: number_of_pcr_cycles_for_indexing

Library preparation kit
type: AnnotationProperty
definition: Reagent kit used for library preparation
preferred label: library_preparation_kit

Sample indexing kit
type: AnnotationProperty
definition: Indexes are needed for multiplexing sequencing libraries for simultaneous sequencing (pooling) and proper attachment to the Illumina flowcell. Each indexing kit would have a number of compatible sequences ("sample indexing sets") that are used to label some number of samples (the number of sets depend on the kit).
preferred label: sample_indexing_kit

Sample indexing set
type: AnnotationProperty
definition: The specific sequencing barcode index set used, selected from the sample indexing kit.
preferred label: sample_indexing_set

Is technical replicate?
type: AnnotationProperty
definition: Is the sequencing reaction run in replicate, "Yes" or "No". If "Yes", FASTQ files in dataset need to be merged.
preferred label: is_technical_replicate

Expected entity capture count
type: AnnotationProperty
definition: Number of cells, nuclei or capture spots expected to be captured by the assay. For Visium this is the total number of spots covered by tissue, within the capture area.
preferred label: expected_entity_capture_count

Actual entity input count
type: AnnotationProperty
definition: Number of cell or nuclei input to the assay. This should be included when available.
preferred label: actual_entity_input_count

Barcode offset
type: AnnotationProperty
definition: Position in the read at which the cell or capture spot barcodes start. Cell and capture spot barcodes are, for example, 3 x 8 bp sequences that are spaced by constant sequences (the offsets). First barcode at position 0, then 38, then 76. This should be included when constructing sequencing libraries with a non-commercial kit.
preferred label: barcode_offset

Barcode read
type: AnnotationProperty
definition: Which read file contains the cell or capture spot barcode. This should be included when constructing sequencing libraries with a non-commercial kit. This field is required if the source material is barcoded. This field is used to determine which analysis pipeline to run.
preferred label: barcode_read

Barcode size
type: AnnotationProperty
definition: Length of the cell or capture spot barcode in base pairs. Cell and capture spot barcodes are, for example, 3 x 8 bp sequences that are spaced by constant sequences, the offsets. This should be included when constructing sequencing libraries with a non-commercial kit. This field is required if the source material is barcoded. This field is used to determine which analysis pipeline to run.
preferred label: barcode_size

UMI offset
type: AnnotationProperty
definition: Position in the read at which the umi barcode starts. This should be included when constructing sequencing libraries with a non-commercial kit.
preferred label: umi_offset

UMI read
type: AnnotationProperty
definition: Which read file contains the UMI barcode. This should be included when constructing sequencing libraries with a non-commercial kit.
preferred label: umi_read

UMI size
type: AnnotationProperty
definition: Length of the umi barcode in base pairs. This should be included when constructing sequencing libraries with a non-commercial kit. This field is required if UMI are present. This field is used to determine which analysis pipeline to run.
preferred label: umi_size

Sequencing reagent kit
type: AnnotationProperty
definition: Reagent kit used for sequencing.
preferred label: sequencing_reagent_kit

Sequencing read format
type: AnnotationProperty
definition: Number of sequencing cycles in each round of sequencing (i.e., Read1, i7 index, i5 index, and Read2). This is reported as a comma-delimited list.
preferred label: sequencing_read_format

Transposition reagent kit
type: AnnotationProperty
definition: If Tn5 came from a kit, provide the kit details. This should be set to "Not applicable" if a custom or in-house kit was used.
preferred label: transposition_reagent_kit

Transposition method
type: AnnotationProperty
definition: Modality of capturing accessible chromatin molecules. For example, this would be the type of kit that was used.
preferred label: transposition_method

Sequencing batch ID
type: AnnotationProperty
definition: The ID for the sequencing run. This could, for example, be the chip ID and should allow users the ability to determine which samples were processed together in a sequencing run. It is recommended that data providers prefix the ID with the center name, to prevent values overlapping across centers.
preferred label: sequencing_batch_id

Capture batch ID
type: AnnotationProperty
definition: A lab-generated ID to identify which cells were captured at the same time. This would, for example, be an ID to denote which datasets were derived from a single 10X Genomics Chromium Controller run. In the case of the 10X Controller this could be the chip ID and would allow users the ability to determine which samples were processed together in a Chromium controller. It is recommended that data providers prefix the ID with the center name, to prevent values overlapping across centers.
preferred label: capture_batch_id

Number of pre-amplification PCR cycles
type: AnnotationProperty
definition: The number of PCR cycles run after the Chromium controller step and prior to separating the suspension and initiating library construction.
preferred label: number_of_pre_amplification_pcr_cycles

Assay input unit
type: AnnotationProperty
definition: Units of assay input amount
preferred label: assay_input_unit

Assay input entity
type: AnnotationProperty
definition: This is the entity from which the analyte is being captured. For example, for bulk sequencing this would be "tissue", while it would be "single cell" for single cell sequencing. This field is used to determine which analysis pipeline to run.
preferred label: assay_input_entity

Number of input cells or nuclei
type: AnnotationProperty
definition: How many cells or nuclei were input to the assay? This is typically not available for preparations working with bulk tissue.
preferred label: number_of_input_cells_or_nuclei

Preparation instrument kit
type: AnnotationProperty
definition: The reagent kit used with the preparation instrument.
preferred label: preparation_instrument_kit

Amount of input analyte value
type: AnnotationProperty
definition: The amount of RNA or DNA input to the assay, typically measured by a Qubit, BioAnalyzer, or TapeStation. In most single cell/nuclei assays, this value isn't available.
preferred label: amount_of_input_analyte_value

Amount of input analyte unit
type: AnnotationProperty
definition: Units of amount of entity input to assay value
preferred label: amount_of_input_analyte_unit

Number of iterations of cDNA amplification
type: AnnotationProperty
definition: This is the amplification of the cDNA prior to library construction. This is typically a PCR amplification, while for linear amplification methods like aRNA this would be the number of rounds of aRNA.
preferred label: number_of_iterations_of_cdna_amplification

Mapped area value
type: AnnotationProperty
definition: For Visium, this is the area of spots that was covered by tissue within the captured area, not the total possible captured area which is fixed. For GeoMx this would be the area of the AOI being captured. For HiFi this is the summed area of the ROIs in a single flowcell lane. For CosMx, Xenium and Resolve, this is the area of the FOV (aka ROI) region being captured.
preferred label: mapped_area_value

Mapped area unit
type: AnnotationProperty
definition: The unit of measurement for the mapping area. For Visium and GeoMx this is typically um^2.
preferred label: mapped_area_unit

Spot size value
type: AnnotationProperty
definition: Area of a spot in a Visium or HiFi capture area.
preferred label: spot_size_value

Spot size unit
type: AnnotationProperty
definition: The unit for spot size value.
preferred label: spot_size_unit

Number of spots
type: AnnotationProperty
definition: Number of capture spots within the mapped area. For Visium this would be the number of spots covered by tissue, while it's the number of spots within ROIs for HiFi.
preferred label: number_of_spots

Spot spacing value
type: AnnotationProperty
definition: Approximate center-to-center distance between capture spots. Synonyms: Inter-Spot distance, Spot resolution, Pit size.
preferred label: spot_spacing_value

Spot spacing unit
type: AnnotationProperty
definition: Units corresponding to inter-spot distance.
preferred label: spot_spacing_unit

Capture area ID
type: AnnotationProperty
definition: Which capture area on the slide was used. For Visium this would be [A1, B1, C1, D1]. For HiFi this would be the lane on the flowcell.
preferred label: capture_area_id

Permeabilization time value
type: AnnotationProperty
definition: Permeabilization time used for this tissue section.
preferred label: permeabilization_time_value

Permeabilization time unit
type: AnnotationProperty
definition: The unit for the permeabilization time.
preferred label: permeabilization_time_unit

RNA probe panel
type: AnnotationProperty
definition: This is the probe panel used to target genes. If a custom panel is used, then the list of target gene needs to be uploaded with the dataset files.
preferred label: rna_probe_panel

Is custom probes used?
type: AnnotationProperty
definition: State ("Yes" or "No") whether custom RNA or antibody probes were used. If custom probes are used, a file including the panel components must be included.
preferred label: is_custom_probes_used

MS ionization technique
type: AnnotationProperty
definition: The ionization approach (i.e., sample probing method) for performing imaging mass spectrometry.
preferred label: ms_ionization_technique

Mass analysis polarity
type: AnnotationProperty
definition: The polarity of the mass analysis (positive or negative ion modes).
preferred label: mass_analysis_polarity

Mass-to-charge range low value
type: AnnotationProperty
definition: The low value of the scanned mass-to-charge range, for MS1. (unitless)
preferred label: mass_to_charge_range_low_value

Mass-to-charge range high value
type: AnnotationProperty
definition: The high value of the scanned mass-to-charge range, for MS1. (unitless)
preferred label: mass_to_charge_range_high_value

Mass resolving power
type: AnnotationProperty
definition: The mass resolving power m/∆m, where ∆m is defined as the full width at half-maximum (FWHM) for a given peak with a specified mass-to-charge (m/z). (unitless)
preferred label: mass_resolving_power

Mass-to-charge resolving power
type: AnnotationProperty
definition: The peak (m/z) used to calculate the resolving power.
preferred label: mass_to_charge_resolving_power

Ion mobility
type: AnnotationProperty
definition: Specifies which technology was used for ion mobility spectrometry. Technologies for measuring ion mobility: Traveling Wave Ion Mobility Spectrometry (TWIMS), Trapped Ion Mobility Spectrometry (TIMS), High Field Asymmetric waveform ion Mobility Spectrometry (FAIMS), Drift Tube Ion Mobility Spectrometry (DTIMS), Structures for Lossless Ion Manipulations (SLIM), and cyclic Ion Mobility Spectrometry (cIMS).
preferred label: ion_mobility

MS scan mode
type: AnnotationProperty
definition: MS (mass spectrometry) scan mode refers to the number of steps in the separation of fragments.
preferred label: ms_scan_mode

Matrix deposition method
type: AnnotationProperty
definition: Common methods of depositing matrix for assisting in desorption and ionization in imaging mass spectrometry include robotic spotting, electrospray deposition, and sublimation.
preferred label: matrix_deposition_method

Preparation matrix
type: AnnotationProperty
definition: The matrix is a compound of crystallized molecules that acts like a buffer between the sample and the ionizing probe. It also helps ionize the sample, carrying it along the flight tube so it can be detected.
preferred label: preparation_matrix

Desorption solvent
type: AnnotationProperty
definition: Solvent composition for conducting nanospray desorption electrospray ionization (nanoDESI) or desorption electrospray ionization (DESI).
preferred label: desorption_solvent

Desorption solvent flow rate value
type: AnnotationProperty
definition: The rate of flow of the solvent into a spray.
preferred label: desorption_solvent_flow_rate_value

Desorption solvent flow rate unit
type: AnnotationProperty
definition: Units of the rate of solvent flow.
preferred label: desorption_solvent_flow_rate_unit

Analysis protocol DOI
type: AnnotationProperty
definition: A DOI to a protocols.io protocol describing the software and database(s) used to process the raw data.
preferred label: analysis_protocol_doi

Data collection mode
type: AnnotationProperty
definition: Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition), DIA (Data-independent acquisition), MRM (multiple reaction monitoring), or PRM (parallel reaction monitoring).
preferred label: data_collection_mode

Label name
type: AnnotationProperty
definition: If the samples were labeled (e.g. TMT), provide the name/ID of the label on this sample. Leave blank if not applicable.
preferred label: label_name

LC instrument vendor
type: AnnotationProperty
definition: The manufacturer of the instrument used for liquid chromatography.
preferred label: lc_instrument_vendor

LC instrument model
type: AnnotationProperty
definition: The model number/name of the instrument used for liquid chromatography.
preferred label: lc_instrument_model

LC column vendor
type: AnnotationProperty
definition: The manufacturer of the liquid chromatography column unless self-packed, pulled tip capillary is used.
preferred label: lc_column_vendor

LC column model
type: AnnotationProperty
definition: The model number/name of the liquid chromatography column. If it is a custom self-packed, pulled tip capillary is used enter “Pulled tip capilary”.
preferred label: lc_column_model

LC resin
type: AnnotationProperty
definition: Details of the resin used for liquid chromatography, including vendor, particle size, pore size.
preferred label: lc_resin

LC column length value
type: AnnotationProperty
definition: Liquid chromatography column length.
preferred label: lc_column_length_value

LC column length unit
type: AnnotationProperty
definition: Units for liquid chromatography column length (typically cm).
preferred label: lc_column_length_unit

LC temperature value
type: AnnotationProperty
definition: Liquid chromatography temperature.
preferred label: lc_temperature_value

LC temperature unit
type: AnnotationProperty
definition: Units for liquid chromatography temperature.
preferred label: lc_temperature_unit

LC inner diameter value
type: AnnotationProperty
definition: Liquid chromatography column inner diameter.
preferred label: lc_inner_diameter_value

LC inner diameter unit
type: AnnotationProperty
definition: Units of liquid chromatography column inner diameter (typically microns).
preferred label: lc_inner_diameter_unit

LC flow rate value
type: AnnotationProperty
definition: Value of flow rate.
preferred label: lc_flow_rate_value

LC flow rate unit
type: AnnotationProperty
definition: Units of flow rate.
preferred label: lc_flow_rate_unit

LC gradient value
type: AnnotationProperty
definition: Liquid chromatography gradient.
preferred label: lc_gradient_value

LC gradient unit
type: AnnotationProperty
definition: Unit for liquid chromatography gradient.
preferred label: lc_gradient_unit

LC mobile phase A
type: AnnotationProperty
definition: Composition of mobile phase A.
preferred label: lc_mobile_phase_a

LC mobile phase B
type: AnnotationProperty
definition: Composition of mobile phase B.
preferred label: lc_mobile_phase_b

Spatial sampling technique
type: AnnotationProperty
definition: Specifies whether or not the analysis was performed in a spatialy targeted manner and the technique used for spatial sampling. For example, Laser-capture microdissection (LCM), Liquid Extraction Surface Analysis (LESA), Nanodroplet Processing in One pot for Trace Samples (nanoPOTS).
preferred label: spatial_sampling_technique

Spatial sampling type
type: AnnotationProperty
definition: Specifies whether or not the analysis was performed in a spatially targeted manner. Spatial profiling experiments target specific tissue foci but do not necessarily generate images. Spatial imaging expriments collect data from a regular array (pixels) that can be visualized as heat maps of ion intensity at each location (molecular images). Leave blank if data are derived from bulk analysis.
preferred label: spatial_sampling_type

Spatial samping target
type: AnnotationProperty
definition: Specifies the cell-type or functional tissue unit (FTU) that is targeted in the spatial profiling experiment. Leave blank if data are generated in imaging mode without a specific target structure.
preferred label: spatial_samping_target

Target retrieval incubation temperature
type: AnnotationProperty
definition: The temperature in Celsius. This will normally be 100 degrees Celsius for RNA assays, and 80 degrees Celsius for protein assays.
preferred label: target_retrieval_incubation_temperature

Target retrieval incubation time value
type: AnnotationProperty
definition: The duration for which a sample is exposed to a target retrieval solution.
preferred label: target_retrieval_incubation_time_value

Target retrieval incubation time unit
type: AnnotationProperty
definition: The units for target retrieval incubation time value.
preferred label: target_retrieval_incubation_time_unit

ProteinaseK concentration
type: AnnotationProperty
definition: The amount or concentration of the enzyme Proteinase K within a sample (in ug/ml).
preferred label: proteinasek_concentration

ProteinaseK incubation time value
type: AnnotationProperty
definition: The duration for which a sample is exposed to Proteinase K.
preferred label: proteinasek_incubation_time_value

ProteinaseK incubation time unit
type: AnnotationProperty
definition: The units for proteinaseK incubation time value.
preferred label: proteinasek_incubation_time_unit

Region of interest label
type: AnnotationProperty
definition: A label for the region of interest. For Xenium, Resolve and CosMx, this is the field of view (FOV) label. For GeoMx this can be found in the "Initial Dataset" spreadsheet (download from within Data Analysis Suite).
preferred label: region_of_interest_label

Anatomical structure label
type: AnnotationProperty
definition: Name of the overarching anatomical structure.
preferred label: anatomical_structure_label

Anatomical structure ID
type: AnnotationProperty
definition: The ontology ID for the overarching anatomical structure. Typically this would be an UBERON ID.
preferred label: anatomical_structure_id

ROI description
type: AnnotationProperty
definition: A description of the anatomical structure being captured in the region of interest (ROI).
preferred label: roi_description

ROI ID
type: AnnotationProperty
definition: Multiple images are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1 to N representing the ROI captured on a slide.
preferred label: roi_id

Acquisition ID
type: AnnotationProperty
definition: The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image.
preferred label: acquisition_id

Area normalized ion dose value
type: AnnotationProperty
definition: Number of primary ions delivered to the sample per unit area.
preferred label: area_normalized_ion_dose_value

Area normalized ion dose unit
type: AnnotationProperty
definition: Area normalized ion dose unit.
preferred label: area_normalized_ion_dose_unit

Data precision bytes
type: AnnotationProperty
definition: Numerical data precision in bytes.
preferred label: data_precision_bytes

Pixel dwell time value
type: AnnotationProperty
definition: Resident time of primary ion beam on each pixel to ionize it.
preferred label: pixel_dwell_time_value

Pixel dwell time unit
type: AnnotationProperty
definition: Pixel dwell time unit.
preferred label: pixel_dwell_time_unit

Antibodies path
type: AnnotationProperty
definition: This is the location of the antibodies.tsv file relative to the root of the top level of the upload directory structure. This path should begin with "." and would likely be something like "./extras/antibodies.tsv".
preferred label: antibodies_path

Ablation frequency unit
type: AnnotationProperty
definition: Frequency unit of laser ablation.
preferred label: ablation_frequency_unit

Ablation frequency value
type: AnnotationProperty
definition: Frequency value of laser ablation.
preferred label: ablation_frequency_value

Antibody concentration unit
type: AnnotationProperty
definition: The concentration units of the antibody preparation. Leave blank if not applicable.
preferred label: antibody_concentration_unit

Channel ID
type: AnnotationProperty
definition: Structure of the identifier depends on the acquisition system. Whenever possible this should exactly match the channel ID in the OME TIFF file. For example the channel ID in an OME TIFF might be something like "Channel:0:13" which would then be the value entered here.
preferred label: channel_id

HGNC symbol
type: AnnotationProperty
definition: Gene symbol approved by HGNC (https://www.genenames.org/) for target gene.
preferred label: hgnc_symbol

Antibody RRID
type: AnnotationProperty
definition: The RRID is a unique antibody identifier that comes from the Antibody Registry (https://antibodyregistry.org). If needed, more info available here: https://www.antibodyregistry.org/faq. Example: AB_10002075
preferred label: antibody_rrid

Uniprot accession number
type: AnnotationProperty
definition: A unique identifier for the target protein in the UniProt database (https://www.uniprot.org).
preferred label: uniprot_accession_number

Lot number
type: AnnotationProperty
definition: The lot number is specific to the vendor. Example: Abcam lot number is GR3238979-1
preferred label: lot_number

Dilution factor
type: AnnotationProperty
definition: Dillution factor is a whole number. Ratio of stock antibody in the experimental solution, with numerator of 1 assumed. e.g. for a 1:200 (1/200) dilution, the dilution factor would be 200.
preferred label: dilution_factor

Antibody concentration value
type: AnnotationProperty
definition: The concentration value of the antibody preparation. Leave blank if not applicable.
preferred label: antibody_concentration_value

Conjugated cat number
type: AnnotationProperty
definition: An antibody may be conjugated to a fluorescent tag or a metal tag for detection. Conjugated antibodies may be purchased from commercial providers. Leave blank if not applicable.
preferred label: conjugated_cat_number

Conjugated tag
type: AnnotationProperty
definition: The name of the entity conjugated to the antibody. Leave blank if not applicable.
preferred label: conjugated_tag

ROI segmentation strategy
type: AnnotationProperty
definition: The method of segmentation that was applied in a GeoMx assay. If an overlay was used the overlay image needs to be included in the dataset upload.
preferred label: roi_segmentation_strategy

Probe hybridization time unit
type: AnnotationProperty
definition: The units for probe hybridization time value.
preferred label: probe_hybridization_time_unit

Oligo probe panel
type: AnnotationProperty
definition: This is the probe panel used to target genes and/or proteins. In cases where there is a core panel and add-on modules, the core panel should be selected here. If additional panels are used, then they must be included in the "additional_panels_used.csv" file that's uploaded with the dataset.
preferred label: oligo_probe_panel

Restricted files
type: AnnotationProperty
definition: A semicolon separated list of non-shared files to be included in the dataset. The path assumes the files are located in the "TOP/non-global/" directory. For example, for the file is TOP/non-global/lab_processed/images/1-tissue-boundary.geojson the value of this field would be "./lab_processed/images/1-tissue-boundary.geojson". After ingest, these files will be copied to the appropriate locations within the respective dataset directory tree. This field is used for internal HuBMAP processing. Examples for GeoMx and PhenoCycler are provided in the File Locations documentation: https://docs.google.com/document/d/1n2McSs9geA9Eli4QWQaB3c9R3wo5d5U1Xd57DWQfN5Q/edit#heading=h.1u82i4axggee
preferred label: restricted_files

Cell boundary marker or stain
type: AnnotationProperty
definition: If a marker or stain was used to identify all cell boundaries in the tissue, then the name of the marker or stain should be included here. The name of the antibody-targeted molecule marker or non-antibody targeted molecule stain included here must be identical to what is found in the imaging data. For example, with the PhenoCycler, this name must match the value found in the XPD output file. If multiple marker or stains are used to identify all cell boundaries, then a comma separated list should be used here.
preferred label: cell_boundary_marker_or_stain

Nuclear marker or stain
type: AnnotationProperty
definition: If a marker or stain was used to identify all nulcei in the tissue (e.g., DAPI), then the name of the marker or stain should be included here. The name of the antibody-targeted molecule marker or non-antibody targeted molecule stain included here must be identical to what is found in the imaging data. For example, with the PhenoCycler, this name must match the value found in the XPD output file. If multiple marker or stains are used to identify all nuclei, then a comma separated list should be used here.
preferred label: nuclear_marker_or_stain

Parent dataset ID
type: AnnotationProperty
definition: Unique HuBMAP or SenNet identifier of the dataset(s) used to generate this EPIC. For example, for a segmentation mask, the parent would be the imaging assay that contains the OME TIFF file used. If an EPIC comes from multiple parent datasets then this should be a comma separated list. Example: HBM386.ZGKG.235, HBM672.MKPK.442 or SNT232.UBHJ.322, SNT329.ALSK.102
preferred label: parent_dataset_id

Derived dataset protocol DOI
type: AnnotationProperty
definition: DOI for the protocols.io page that describes the analysis performed when generating this EPIC dataset. For example for an EPIC analysis of a sequencing dataset, the protocol should include the pipeline run, reference libraries used, and URLs for critical programs.
preferred label: derived_dataset_protocol_doi

Derived dataset type
type: AnnotationProperty
definition: The specific type of EPIC analysis being executed.
preferred label: derived_dataset_type

Primary dataset type
type: AnnotationProperty
definition: The type of primary dataset used to derive this EPIC.
preferred label: primary_dataset_type

Number of files containing masks
type: AnnotationProperty
definition: How many OME TIFF files are included. Each OME TIFF file can contain multiple masks. Masks with different bit depths should be contained in different OME TIFF files. For example a 32-bit mask used for cell idenfication would be in one OME TIFF file, while an 8-bit mask denoting FTUs would be in a second OME TIFF file. This field captures the total number of OME TIFF files.
preferred label: number_of_files_containing_masks

Number of masks
type: AnnotationProperty
definition: How many masks are included, inclusive of all OME TIFF files.
preferred label: number_of_masks

Target name
type: AnnotationProperty
definition: This is the name of the protein that the antibody is targeting. Please list the UniProt protein name. This may be different from the common name for the protein.
preferred label: target_name

Isotype
type: AnnotationProperty
definition: Describes the antibody isotype. Please write out any symbols. (e.g. IgG, IgG1, IgG1 kappa)
preferred label: isotype

Host
type: AnnotationProperty
definition: This is the species that was used to generate the antibody (e.g. mouse, rabbit, etc).
preferred label: host

Clonality
type: AnnotationProperty
definition: This will be either Monoclonal or Polyclonal.If monoclonal provide the clone ID or identify the antibody as polyclonal.
preferred label: clonality

Antibody vendor
type: AnnotationProperty
definition: This is the company that sells the antibody.
preferred label: antibody_vendor

Catalog number
type: AnnotationProperty
definition: Provides catalog number from vendor for the source of the antibody.
preferred label: catalog_number

Recombinant
type: AnnotationProperty
definition: Simple Yes or No if the antibody was recombinant. Recombinant antibodies (rAbs) are monoclonal antibodies which are generated in vitro using synthetic genes.
preferred label: recombinant

Assay method
type: AnnotationProperty
definition: This is the downstream assay that was used (e.g. CODEX, MIBI, etc).
preferred label: assay_method

Tissue preservation technique
type: AnnotationProperty
definition: Preservation technique used. If fixative other than formalin, indicate the percentage of fixative indicated (e.g., 1% or 4%). Use a common abbreviation format (e.g., FFPE for formalin fixed paraffin embedded).
preferred label: tissue_preservation_technique

Author ORCID
type: AnnotationProperty
definition: This is needed for whomever is submitting the validation data. This will be used to differentiate the same antibodies being tested across different groups. Identifies the individual who validated the antibody used in the assay; Format ####-####-####-#### (the last digit may be X) See https://info.orcid.org/researchers/
preferred label: author_orcid

Vendor affiliation
type: AnnotationProperty
definition: Identities whether the antibody validation was done by commercial entity (antibody vendor or multiplexed technology provider). Vendor name. If not applicable, please leave this field blank. (e.g. Cell Signaling Technology, Bio-Techne, Abcam, Biolegend, Akoya Biosciences, Leica Microsystems)
preferred label: vendor_affiliation

Organ name
type: AnnotationProperty
definition: This is the tissue that was used to acquire the validation data. This should be the same tissue that was used in the downstream assay.
preferred label: organ_name

Antigen retrieval
type: AnnotationProperty
definition: If applicable, indicate general conditions under which antigen retrieval was performed. Additional details should be available in the referenced protocol (see protocol_doi field).Required format: pH values; if multiple, separate by commas.
preferred label: antigen_retrieval

AVR filename
type: AnnotationProperty
definition: The name of the corresponding AVR document in PDF format that this row of metadata is associated with. This name must match the file uploaded in the Antibody PDF section of the AVR upload screen during submission.
preferred label: avr_filename

OMAP ID
type: AnnotationProperty
definition: Unique identifier assigned to Organ Mapping Antibody Panel (OMAP) at time of publication. OMAP with number based on date created (e.g. OMAP-1, OMAP-2) (optional field)
preferred label: omap_id

Cycle number
type: AnnotationProperty
definition: Identifies the cycle number in which an antibody was either applied to the tissue or, in the case of CODEX,visualized with a fluorescent reporter. For non-cyclic methods use 1 for all cycles. Required field if AVR is part of an Organ Mapping Antibody Panel (OMAP).
preferred label: cycle_number

Fluorescent reporter
type: AnnotationProperty
definition: For indirect visualization (e.g., oligo-conjugated antibodies), define the fluorescent reporter utilized in the corresponding cycle. For metal or fluorophore-conjugated antibodies, please leave blank. Required field if AVR is part of an Organ Mapping Antibody Panel (OMAP).
preferred label: fluorescent_reporter

Is channel used for nuclei segmentation?
type: AnnotationProperty
definition: Specifies if this channel can be used by algorithms performing nuclei segmentation ("Yes" or "No").
preferred label: is_channel_used_for_nuclei_segmentation

Is channel used for cell segmentation?
type: AnnotationProperty
definition: Specifies if this channel can be used by algorithms performing cell segmentation ("Yes" or "No").
preferred label: is_channel_used_for_cell_segmentation

Is antibody
type: AnnotationProperty
definition: Does this channel encode image intensities associated with an antibody ("Yes" or "No")? If "Yes" then the relevant antibody is expected to be listed in the antibodies.tsv file with the same channel ID.
preferred label: is_antibody

Antibody reagent kit
type: AnnotationProperty
preferred label: antibody_reagent_kit

Viability reagent kit
type: AnnotationProperty
preferred label: viability_reagent_kit

Instrument calibration bead kit
type: AnnotationProperty
preferred label: instrument_calibration_bead_kit

Loaded cell concentration unit
type: AnnotationProperty
preferred label: loaded_cell_concentration_unit

Chemistry kit
type: AnnotationProperty
preferred label: chemistry_kit

Pixel physical size height unit
type: AnnotationProperty
preferred label: pixel_physical_size_height_unit

Pixel physical size width unit
type: AnnotationProperty
preferred label: pixel_physical_size_width_unit

Pixel physical size depth unit
type: AnnotationProperty
preferred label: pixel_physical_size_depth_unit

Capture area width unit
type: AnnotationProperty
preferred label: capture_area_width_unit

Capture area height unit
type: AnnotationProperty
preferred label: capture_area_height_unit

Spatial discretization method
type: AnnotationProperty
preferred label: spatial_discretization_method

Signal quenching method
type: AnnotationProperty
preferred label: signal_quenching_method

Concept
type: Class
subclass of: Thing
prefix IRI: skos:Concept

ConceptScheme
type: Class
subclass of: Thing
prefix IRI: skos:ConceptScheme

Magnetic resonance
type: NamedIndividual
type: Concept
broader: Modality
definition: An acquisition device, process or method that performs magnetic resonance imaging.
preferred label: Magnetic Resonance

Aspen chip bedding
type: NamedIndividual
type: Concept
broader: Bedding
definition: Organism housed with bedding made from all natural aspen chips.

Aspen shaving bedding
type: NamedIndividual
type: Concept
broader: Bedding
definition: Organism housed with bedding made from all natural aspen shavings.

Corn cob bedding
type: NamedIndividual
type: Concept
broader: Bedding
definition: Organism housed with bedding made from ground corn cobs.

Pine chip bedding
type: NamedIndividual
type: Concept
broader: Bedding
definition: Organism housed with bedding made from all natural pine chips.

Pine shaving bedding
type: NamedIndividual
type: Concept
broader: Bedding
definition: Organism housed with bedding made from all natural pine shavings.

Laser ablation
type: NamedIndividual
type: Concept
broader: MS ionization technique
definition: Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by light amplification by stimulated emission of radiation.
preferred label: LA

Healthy
type: NamedIndividual
type: Concept
broader: Organ condition
definition: Having no significant health-related issues.

Cell
type: NamedIndividual
type: Concept
broader: Suspension entity type
definition: The smallest units of living structure capable of independent existence, composed of a membrane-enclosed mass of protoplasm and containing a nucleus or nucleoid.

In house
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: Acquisition instrument model
broader: Preparation instrument vendor
broader: LC instrument vendor
broader: LC column vendor
definition: Created, done, or existing within a company or organization.
preferred label: In-House

Nucleus
type: NamedIndividual
type: Concept
broader: Suspension entity type
definition: A body within the cell, surrounded by a membrane, within which lie the chromosomes, one or more nucleoli, combined with proteins, and exhibits mitosis.

Chromatin
type: NamedIndividual
type: Concept
broader: Analyte class
definition: The genetic material of the nucleus, consisting of deoxyribonucleoprotein, which occurs in two forms during the phase between mitotic divisions: 1) as heterochromatin, seen as condensed, readily stainable clumps; 2) as euchromatin, dispersed lightly staining or nonstaining material. During mitotic division the chromatin condenses into chromosomes.

Formalin-fixed paraffin-embedded
type: NamedIndividual
type: Concept
broader: Storage medium
definition: Refers to a process where a sample is preserved with formalin and then embedded into a paraffin block for sectioning.
preferred label: FFPE (Paraffin embedded)

Thermal Ionization Mass Spectrometry
type: NamedIndividual
type: Concept
broader: Ion mobility
definition: A mass spectrometry method in which chemically-purified samples are heated to create positively ionized atoms that are then accelerated by an electric field and mass separated by an electromagnet.
preferred label: TIMS

Data-Dependent Acquisition
type: NamedIndividual
type: Concept
broader: Data collection mode
definition: A method for collecting tandem mass spectrometry data where the m/z values are prerecorded for a fixed number of precursor ions followed by a second stage of mass spectrometry and m/z analysis.
preferred label: DDA

Data-Independent Acquisition
type: NamedIndividual
type: Concept
broader: Data collection mode
definition: A method for collecting tandem mass spectrometry data where the m/z values for all the ions are fragmented and analyzed during the second stage of spectrometry
preferred label: DIA

Selected Reaction Monitoring
type: NamedIndividual
type: Concept
broader: Data collection mode
definition: A method for collecting tandem mass spectrometry data where an ion of a particular mass is selected in the first stage and a fragmented ion product is selected in the second mass spectrometer stage for detection. Selected reaction monitoring (SRM)-based experiments are generally performed in a triple quadrupole (QqQ) mass spectrometer.
preferred label: SRM

Parallel Reaction Monitoring
type: NamedIndividual
type: Concept
broader: Data collection mode
definition: A method for collecting tandem mass spectrometry data where an ion of a particular mass is selected in the first stage and a fragmented ion product is selected in the second mass spectrometer stage for detection. Parallel reaction monitoring (PRM)-based experiments are generally performed in a high-resolution hybrid quadrupole-Orbitrap (Q-OT) or time-of-flight mass spectrometer.
preferred label: PRM

Collagen
type: NamedIndividual
type: Concept
broader: Analyte class
definition: A family of large fibrous proteins that are the main components of connective tissue and are responsible for maintaining tissue structure.

Protein
type: NamedIndividual
type: Concept
broader: Analyte class
definition: A group of complex organic macromolecules composed of one or more chains (linear polymers) of alpha-L-amino acids linked by peptide bonds and ranging in size from a few thousand to over 1 million Daltons. Proteins are fundamental genetically encoded components of living cells with specific structures and functions dictated by amino acid sequence.

Read pair 1
type: NamedIndividual
type: Concept
broader: Barcode read
broader: UMI read
definition: The read direction identified as number 1 in a paired-end nucleotide sequencing reaction.
preferred label: Read 1 (R1)

Read pair 2
type: NamedIndividual
type: Concept
broader: Barcode read
broader: UMI read
definition: The read direction identified as number 2 in a paired-end nucleotide sequencing reaction.
preferred label: Read 2 (R2)

Diseased
type: NamedIndividual
type: Concept
broader: Organ condition
definition: An indication that an anatomic structure has detectable aberrations.

NP40 Lysis Buffer
type: NamedIndividual
type: Concept
broader: Preparation medium
definition: A detergent-based cell lysis buffer suitable for total protein extraction. The formulation helps retain the protein structure and function for enzyme assays or immunoassays.
preferred label: Lysis buffer

Roswell Park Memorial Institute 1640 Medium
type: NamedIndividual
type: Concept
broader: Transport solution
definition: RPMI stands for "Roswell Park Memorial Institute." RPMI 1640 is a common type of cell culture medium used in laboratory and research settings, particularly in cell biology, immunology, and cancer research. It is formulated to support the growth and maintenance of various types of mammalian cells in vitro. [Generated by an AI language model]
preferred label: RPMI

Unknown
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Preparation condition
broader: Storage medium
broader: Storage method
broader: Acquisition instrument model
broader: Organ condition
broader: Perfusion solution
broader: Transport solution
definition: Not known, observed, recorded; or reported as unknown by the data contributor.

PAXgene tissue system
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium
definition: A proprietary system comprised of a formalin-free tissue fixative and stabilizing reagent designed to preserve tissue structures without damaging biomolecules. This allows both histologic examination and isolation of RNA, miRNA, DNA, and/or proteins from a single sample.
preferred label: PAXgene tissue kit (PXT)

Liquid nitrogen storage
type: NamedIndividual
type: Concept
broader: Preparation condition
broader: Storage method
definition: An indication that a material has been stored in liquid nitrogen.
preferred label: Frozen in liquid nitrogen

Liquid nitrogen vapor storage
type: NamedIndividual
type: Concept
broader: Preparation condition
broader: Storage method
definition: An indication that a material has been stored in liquid nitrogen vapor.
preferred label: Frozen in liquid nitrogen vapor

Dulbecco's Modified Eagle Medium
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Transport solution
definition: DMEM stands for "Dulbecco's Modified Eagle Medium." DMEM is a commonly used cell culture medium in biological and biomedical research. It's not typically used as a transport solution itself but is often employed as a nutrient-rich medium to maintain and transport cells, tissues, or biological samples. [Generated by an AI language model]
preferred label: DMEM

Frozen on dry ice
type: NamedIndividual
type: Concept
broader: Preparation condition
broader: Storage method
definition: A sample that is in a frozen state maintained with dry ice.

Laser Capture Microdissection
type: NamedIndividual
type: Concept
broader: Spatial sampling technique
definition: A high-resolution method used to isolate cells from their surrounding tissues, with the aid of a laser beam, under direct microscopic visualization. Specific cells can be isolated directly by cutting target cells away from unwanted cells, to obtain enriched cell populations.
preferred label: LCM

Electrospray ionization
type: NamedIndividual
type: Concept
broader: MS ionization technique
definition: A procedure used in mass spectrometry analysis. Means of delivering nonvolatile analytes into the gas phase for mass analysis. Best used on molecules which are charged in solution or readily accept a charge. Particularly well suited to the analysis of biomolecules. Can be used to probe tertiary structure and non-covalent interactions (from NCSU Mass Spectrometry Facility web site)
preferred label: ESI

Cell segmentation
type: NamedIndividual
type: Concept
broader: Spatial discretization method
definition: The computational process of identifying and separating individual cells within an image.

Right
type: NamedIndividual
type: Concept
broader: Laterality
definition: Being or located on or directed toward the side of the body to the east when facing north.

Left
type: NamedIndividual
type: Concept
broader: Laterality
definition: Being or located on or directed toward the side of the body to the west when facing north.

cDNA
type: NamedIndividual
type: Concept
broader: Suspension entity type
definition: Single-stranded DNA that is complementary to messenger RNA or DNA that has been synthesized from messenger RNA by reverse transcriptase.

None
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium
broader: Storage method
broader: Perfusion solution
broader: Transport solution
broader: Viability reagent kit
broader: Instrument calibration bead kit
definition: No person or thing, nobody, not any.

Hertz
type: NamedIndividual
type: Concept
broader: Imaging frequency unit
definition: A SI derived unit of frequency; equal to one oscillation (one cycle) per second.
preferred label: Hz

DNA
type: NamedIndividual
type: Concept
broader: Analyte class
definition: A long linear double-stranded polymer formed from nucleotides attached to a deoxyribose backbone and found in the nucleus of a cell; associated with the transmission of genetic information.

Not applicable
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
broader: Stain technique
broader: Preparation instrument vendor
broader: Preparation instrument model
broader: Tile configuration
broader: Scan direction
broader: Laterality
broader: Sample indexing kit
broader: Barcode read
broader: UMI read
broader: Transposition reagent kit
broader: RNA probe panel
broader: Matrix deposition method
definition: Determination of a value is not relevant in the current context.

Metabolite
type: NamedIndividual
type: Concept
broader: Analyte class
definition: Any substance involved in metabolism, either as a product of metabolism or as necessary for metabolism.

Lipid
type: NamedIndividual
type: Concept
broader: Analyte class
definition: A class of hydrocarbon-containing organic compounds. Lipids are insoluble in water but soluble in nonpolar solvents and play important roles in living organisms: these roles include functioning as energy storage molecules, serving as structural components of cell membranes, and constituting important signaling molecules. Lipids can be subdivided into 2 groups: fatty acids and glycerides.

RNALater
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium
definition: Trade name for an aqueous, non-toxic tissue storage reagent that rapidly permeates tissues to stabilize and protect cellular RNA.
preferred label: RNAlater

Optimal cutting temperature compound
type: NamedIndividual
type: Concept
broader: Storage medium
definition: A solution of water soluble glycols and resins that provide a specimen support matrix for cryostat sectioning at temperatures of -10 degrees C and below.
preferred label: OCT

Water
type: NamedIndividual
type: Concept
broader: Storage medium
definition: H2O, a clear, colorless, odorless, tasteless liquid that freezes into ice below 0 degrees centigrade and boils above 100 degrees centigrade.

Customize
type: NamedIndividual
type: Concept
broader: Preparation instrument model
broader: Library preparation kit
broader: Sample indexing kit
broader: Sequencing reagent kit
broader: Transposition reagent kit
broader: Transposition method
broader: Preparation instrument kit
broader: RNA probe panel
broader: Oligo probe panel
broader: Antibody reagent kit
broader: Viability reagent kit
broader: Instrument calibration bead kit
broader: Chemistry kit
definition: To make according to individual requirements or specifications; to make more personalized or tailored for a specific need.
preferred label: Custom

Gelatin
type: NamedIndividual
type: Concept
broader: Storage medium

Kilohertz
type: NamedIndividual
type: Concept
broader: Imaging frequency unit
definition: A unit of measure denoting the frequency equal to 1000 cycles per second meaning e.g. that the cylical waveform changes from one state to the other (from one polarity to the other) 1000 times per second.
preferred label: kHz

Megahertz
type: NamedIndividual
type: Concept
broader: Imaging frequency unit
definition: The SI derived unit of frequency; equal to one million oscillations per second or to 10E6 hertz.
preferred label: MHz

Specimen at room temperature
type: NamedIndividual
type: Concept
broader: Preparation condition
broader: Storage method
definition: A specimen that has been subjected to and adjusted to the average ambient temperature of a room, usually considered to be around 20 degrees C (68 degrees F).
preferred label: Stored in ambient temperature

Peptide
type: NamedIndividual
type: Concept
broader: Analyte class
definition: A compound of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.

Midline
type: NamedIndividual
type: Concept
broader: Laterality
definition: A medial line, especially the medial line or medial plane of the body (or some part of the body).

RNA
type: NamedIndividual
type: Concept
broader: Analyte class
definition: Single-stranded long chain of nucleotides containing ribose. It is the end product of DNA transcription by the enzyme RNA polymerase. It is essential in protein synthesis.

Carboxymethylcellulose
type: NamedIndividual
type: Concept
broader: Storage medium
preferred label: CMC

Formic acid
type: NamedIndividual
type: Concept
broader: Storage medium
definition: A reagent comprised of the organic chemical formic acid that cleaves proteins into peptides at the C- or N-terminal side of an aspartate residue.
preferred label: Formic acid in water

Male
type: NamedIndividual
type: Concept
broader: Sex
definition: Orgamism is male.

Female
type: NamedIndividual
type: Concept
broader: Sex
definition: Orgamism is female.

Standard/default
type: NamedIndividual
type: Concept
broader: Light cycle
definition: Organism housed with 12-hr light: 12-hr dark (12L: 12D) with the lights ON during the daytime.

Alcian Blue stain with Periodic acid-Schiff
type: NamedIndividual
type: Concept
broader: Stain name
definition: Alcian Blue with Periodic acid-Schiff (AB-PAS) is a dual staining technique used to differentiate between acidic mucins (stained blue by Alcian Blue) and neutral mucins or glycogen (stained magenta by PAS). This combined stain is particularly useful for examining tissues with mucus-secreting cells, aiding in the diagnosis of various gastrointestinal and respiratory tract conditions. [Generated by an AI language model]
preferred label: AB-PAS

Hematoxylin and eosin stain
type: NamedIndividual
type: Concept
broader: Stain name
definition: Hematoxylin is a dark purplish dye that stains the chromatin (nuclear material) within the nucleus. Eosin is an orangish-pink to red dye that stains the cytoplasmic material including connective tissue and collagen.
preferred label: H&E

Luxol fast blue/Cresyl violet stain
type: NamedIndividual
type: Concept
broader: Stain name
definition: An alcohol soluble copper phthalocyanine dye, and cresyl violet, an organic compound that is commonly used as a counter stain, to determine the presence of myelin as well as helicobacter and campylobacter bacterial species.
preferred label: LFB

Periodic acid-Schiff stain
type: NamedIndividual
type: Concept
broader: Stain name
definition: This is an all-round useful stain for many things, including glycogen, mucin, mucoprotein, glycoprotein, as well as fungi. The reaction is based on the oxidation of glycol group to aldehydes by periodate. The schiff's reagent selectively stains the aldehydes to a rose pink color. PAS is useful for outlining tissue structures--basement membranes, capsules, blood vessels, etc.
preferred label: PAS

Sudan black B stain
type: NamedIndividual
type: Concept
broader: Stain name
definition: Sudan Black B is a lipid-soluble dye used to stain lipids within cells and tissues, turning them dark blue to black, which aids in identifying fat deposits and lipid-rich organelles, as well as differentiating certain cell types for diagnostic purposes. [Generated by an AI language model]
preferred label: SBB

Trichrome stain
type: NamedIndividual
type: Concept
broader: Stain name
definition: Acid dyes and washes to selectively dye the structural elements in tissue samples in three or more contrasting colors.
preferred label: Trichrome

Other
type: NamedIndividual
type: Concept
broader: Euthanization method
broader: Room health status
broader: Rack setup
broader: Light cycle
broader: Bedding
broader: Cage enhancements
definition: Organism housed in a room with alternative health status not specified.
definition: Organism housed in cages not specified.
definition: Organism housed with bedding not specified.
definition: Organism housed with light cycle not specified.
definition: Organism housed with nesting/chewing implements not specified.
definition: Organism was euthanized via alternative method not specified.

Periodate-lysine-paraformaldehyde
type: NamedIndividual
type: Concept
broader: Preparation medium
definition: Combination of periodate, lysine and paraformaldehyde; used as a fixative for the study of duodenal mucosa.
preferred label: PLP (Periodate-Lysine-Paraformaldehyde)

4-(dimethylamino)cinnamic acid
type: NamedIndividual
type: Concept
broader: Preparation matrix
preferred label: DMACA (4-(dimethylamino)cinnamic acid)

Photobleaching
type: NamedIndividual
type: Concept
broader: Signal quenching method
definition: Light-induced change in a chromophore, resulting in the loss of its absorption of light of a particular wave length. The photon energy causes a conformational change in the photoreceptor proteins affecting PHOTOTRANSDUCTION. This occurs naturally in the retina (ADAPTATION, OCULAR) on long exposure to bright light. Photobleaching presents problems when occurring in PHOTODYNAMIC THERAPY, and in FLUORESCENCE MICROSCOPY. On the other hand, this phenomenon is exploited in the technique, FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING, allowing measurement of the movements of proteins and LIPIDS in the CELL MEMBRANE.

Ethanol
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium
definition: A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group.

2,5-Dihydroxybenzoic acid
type: NamedIndividual
type: Concept
broader: Preparation matrix
definition: A dihydroxybenzoic acid having the two hydroxy groups at the 2- and 5-positions.
preferred label: 2,5-DHB (2,5-Dihydroxybenzoic acid)

2',5'-Dihydroxyacetophenone
type: NamedIndividual
type: Concept
broader: Preparation matrix
preferred label: 2,5-DHA (2,5-dihydroxyacetophenone)

Methanol
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium
definition: The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group.

Polysaccharide
type: NamedIndividual
type: Concept
broader: Analyte class
definition: A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.

Fluorochrome
type: NamedIndividual
type: Concept
broader: Analyte class
definition: A fluorescent dye used to stain biological specimens.

N-(1-naphthyl)ethylenediamine dihydrochloride
type: NamedIndividual
type: Concept
broader: Preparation matrix
definition: An ethylenediamine dihydrochloride compound having an N-(1-naphthyl) substituent.
preferred label: NEDC (N-(1-naphthyl) ethylenediamine dihydrochloride)

Paraformaldehyde polymer
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium
definition: A poly(oxymethylene) polymer, composed of paraformaldehyde macromolecules.
preferred label: PFA (Paraformaldehyde)

alpha-cyano-4-hydroxycinnamic acid
type: NamedIndividual
type: Concept
broader: Preparation matrix
definition: A monohydroxycinnamic acid that is 4-hydroxycinnamic acid in which the hydrogen alpha- to the carboxy group is replaced by a cyano group. It is used as a matrix in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of peptides and oligonucleotides.
preferred label: CHCA (alpha-cyano-4-hydroxy-cinnamic acid)

9-aminoacridine
type: NamedIndividual
type: Concept
broader: Preparation matrix
definition: An aminoacridine that is acridine in which the hydrogen at position 9 is replaced by an amino group. A fluorescent dyd and topical antiseptic agent, it is used (usually as the hydrochloride salt) in eye drops for the treatment of superficial eye infections.
preferred label: 9-AA (9-aminoacridine)

sinapic acid
type: NamedIndividual
type: Concept
broader: Preparation matrix
definition: A monohydroxycinnamic acid that is cinnamic acid in which the phenyl hydrogens at positions 3, 4, and 5 are replaced by methoxy, hydroxy, and methoxy groups, respectively.
preferred label: SA (sinapic acid)

Matrix-assisted laser desorption ionization
type: NamedIndividual
type: Concept
broader: MS ionization technique
definition: The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization.
preferred label: MALDI

Laser desorption ionization
type: NamedIndividual
type: Concept
broader: MS ionization technique
definition: The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material.
preferred label: LDI

Desorption electrospray ionization
type: NamedIndividual
type: Concept
broader: MS ionization technique
definition: Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure.
preferred label: DESI

Neutral buffered formalin
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium
broader: Transport solution
definition: A processed material that is a mixture of formalin (formaldehyde), phosphates, and water used as a standard fixative for diagnostic preparations.
preferred label: NBF (Neutral Buffered Formalin)

Enzymatic cleavage
type: NamedIndividual
type: Concept
broader: Signal quenching method
definition: A material processing that digests the fraction of input material that is susceptible to that enzyme

paired-end library
type: NamedIndividual
type: Concept
broader: Library layout
definition: is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
preferred label: paired-end

single-end library
type: NamedIndividual
type: Concept
broader: Library layout
definition: A cDNA library that is a collection of short tags from only one end of DNA fragments.
preferred label: single-end

Single-cell ATAC-seq
type: NamedIndividual
type: Concept
broader: Transposition method
definition: An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles.
preferred label: scATACseq

Bulk assay for transposase-accessible chromatin using sequencing
type: NamedIndividual
type: Concept
broader: Transposition method
definition: An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells.
preferred label: bulkATACseq

Nanospray desorption electrospray ionization assay
type: NamedIndividual
type: Concept
broader: MS ionization technique
definition: A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray.
preferred label: nanoDESI

Nanodroplet Processing in One pot for Trace Samples
type: NamedIndividual
type: Concept
broader: Spatial sampling technique
definition: A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the global protein expression.
preferred label: nanoPOTS

Single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing
type: NamedIndividual
type: Concept
broader: Transposition method
definition: An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation.
preferred label: sciATACseq

Phosphate buffered saline solution
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium
broader: Transport solution
definition: Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic).
preferred label: PBS

Decapitation
type: NamedIndividual
type: Concept
broader: Euthanization method
definition: Organism was euthanized by physical removal of head from the body

Intravenous anesthetic euthanasia
type: NamedIndividual
type: Concept
broader: Euthanization method
definition: Organism was euthanized by intravenous injection of anesthetic.

Cervical dislocation
type: NamedIndividual
type: Concept
broader: Euthanization method
definition: Organism was euthanized by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion.

Carbon dioxide inhalant euthanasia
type: NamedIndividual
type: Concept
broader: Euthanization method
definition: Organism was euthanized by inhalation of carbon dioxide.

kilogram
type: NamedIndividual
type: Concept
broader: Tissue weight unit
broader: Weight unit
definition: A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
preferred label: kg

centimeter
type: NamedIndividual
type: Concept
broader: Thickness unit
broader: Pathology distance unit
broader: Height unit
broader: Width unit
broader: Length unit
broader: LC column length unit
broader: LC inner diameter unit
definition: A length unit which is equal to one hundredth of a meter or 10^[-2] m.
preferred label: cm

millimeter
type: NamedIndividual
type: Concept
broader: Thickness unit
broader: Pathology distance unit
broader: Height unit
broader: Width unit
broader: Length unit
broader: LC column length unit
broader: LC inner diameter unit
broader: Capture area width unit
broader: Capture area height unit
broader: Image width unit
broader: Image height unit
broader: Pixel physical size width unit
broader: Pixel physical size height unit
broader: Pixel physical size depth unit
broader: Spacing between slices unit
definition: A length unit which is equal to one thousandth of a meter or 10^[-3] m.
preferred label: mm

micrometer
type: NamedIndividual
type: Concept
broader: Thickness unit
broader: Spot spacing unit
broader: LC column length unit
broader: LC inner diameter unit
broader: Image width unit
broader: Image height unit
broader: Pixel physical size width unit
broader: Pixel physical size height unit
broader: Pixel physical size depth unit
broader: Spacing between slices unit
definition: A length unit which is equal to one millionth of a meter or 10^[-6] m.
preferred label: um

nanometer
type: NamedIndividual
type: Concept
broader: Pixel physical size width unit
broader: Pixel physical size height unit
broader: Pixel physical size depth unit
broader: Spacing between slices unit
definition: A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
preferred label: nm

gram
type: NamedIndividual
type: Concept
broader: Tissue weight unit
broader: Weight unit
definition: A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
preferred label: g

milligram
type: NamedIndividual
type: Concept
broader: Tissue weight unit
broader: Weight unit
definition: A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
preferred label: mg

microgram
type: NamedIndividual
type: Concept
broader: Tissue weight unit
broader: Assay input unit
broader: Amount of input analyte unit
definition: A mass unit which is equal to one millionth of a gram or 10^[-6] g.
preferred label: ug

nanogram
type: NamedIndividual
type: Concept
broader: Library input amount unit
broader: Library output amount unit
broader: Amount of input analyte unit
definition: A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
preferred label: ng

degree Celsius
type: NamedIndividual
type: Concept
broader: LC temperature unit
definition: A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
preferred label: celsius

millisecond
type: NamedIndividual
type: Concept
broader: Pixel dwell time unit
definition: A time unit which is equal to one thousandth of a second or 10^[-3] s.
preferred label: ms

minute
type: NamedIndividual
type: Concept
broader: Source storage duration unit
broader: Processing time unit
broader: Total run time unit
broader: Warm ischemic time unit
broader: Cold ischemic time unit
broader: Permeabilization time unit
broader: LC gradient unit
broader: Target retrieval incubation time unit
broader: ProteinaseK incubation time unit
broader: Probe hybridization time unit
definition: A time unit which is equal to 60 seconds.

hour
type: NamedIndividual
type: Concept
broader: Source storage duration unit
broader: Processing time unit
broader: Total run time unit
broader: Warm ischemic time unit
broader: Cold ischemic time unit
broader: Probe hybridization time unit
definition: A time unit which is equal to 3600 seconds or 60 minutes.

day
type: NamedIndividual
type: Concept
broader: Source storage duration unit
broader: Processing time unit
broader: Time since acquisition instrument calibration unit
definition: A time unit which is equal to 24 hours.

month
type: NamedIndividual
type: Concept
broader: Source storage duration unit
broader: Time since acquisition instrument calibration unit
definition: A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.

year
type: NamedIndividual
type: Concept
broader: Source storage duration unit
broader: Time since acquisition instrument calibration unit
definition: A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days.

nanomolar
type: NamedIndividual
type: Concept
broader: Library concentration unit
definition: A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
preferred label: nM

square millimeter
type: NamedIndividual
type: Concept
broader: Area unit
broader: Mapped area unit
broader: Spot size unit
definition: An area unit which is equal to one millionth of a square meter or 10^[-6] m^[2].
preferred label: mm^2

cubic centimeter
type: NamedIndividual
type: Concept
broader: Volume unit
definition: A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
preferred label: cm^3

milliliter
type: NamedIndividual
type: Concept
broader: Volume unit
definition: A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
preferred label: ml

microliter
type: NamedIndividual
type: Concept
broader: Library input amount unit
broader: Library output amount unit
definition: A volume unit which is equal to one millionth of a liter or 10^[-6] L.
preferred label: ul

hertz
type: NamedIndividual
type: Concept
broader: Ablation frequency unit
definition: A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
preferred label: Hz

microliters per minute
type: NamedIndividual
type: Concept
broader: Desorption solvent flow rate unit
definition: A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
preferred label: uL/min

microgram per milliliter
type: NamedIndividual
type: Concept
broader: Antibody concentration unit
definition: A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters.
preferred label: ug/ml

square micrometer
type: NamedIndividual
type: Concept
broader: Area unit
broader: Mapped area unit
broader: Spot size unit
definition: An area unit which is equal to an area enclosed by a square with sides each 1 micrometer long.
preferred label: um^2

nanogram per microliter
type: NamedIndividual
type: Concept
broader: Library concentration unit
definition: A mass unit density which is equal to mass of an object in nanograms divided by the volume in microliters.
preferred label: ng/ul

monoclonal
type: NamedIndividual
type: Concept
broader: Clonality
definition: Highly specific antibodies produced by the clones of a single hybrid cell, which is generated by the fusion of a B cell with a tumor cell. They recognize a unique epitope of an antigen.
preferred label: Monoclonal

polyclonal
type: NamedIndividual
type: Concept
broader: Clonality
definition: Antibodies produced by immunizing a mammal such as a mouse, rabbit or goat with an antigen. They are a mixture of antibodies produced from different B cells raised against any of the different epitopes of that antigen.
preferred label: Polyclonal

Thermo Fisher Scientific
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: Preparation instrument vendor
broader: LC instrument vendor
broader: LC column vendor
definition: Commercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.

Leica Microsystems
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Leica Microsystems develops and manufactures microscopes and scientific instruments for the analysis of microstructures and nanostructures. Widely recognized for optical precision and innovative technology, the company is one of the market leaders in compound and stereo microscopy, digital microscopy, confocal laser scanning and super-resolution microscopy with related imaging systems, electron microscopy sample preparation, and surgical microscopy.

MilliporeSigma
type: NamedIndividual
type: Concept
broader: LC column vendor
definition: A leading biotechnology supplier that provides research reagents, lab materials, and biomanufacturing solutions supporting the entire drug development process from discovery to production. Formed from the merger of Millipore and Sigma-Aldrich, it serves as a key global partner to biotech and pharmaceutical companies advancing biologics, cell and gene therapies, and other innovative modalities.
preferred label: Millipore

Miltenyi Biotec
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Miltenyi Biotec is a global biotechnology company headquartered in Bergisch Gladbach, Germany, that develops and supplies innovative products and services to support basic and clinical research as well as the advancement of cell and gene therapies. Their portfolio spans cell separation, flow cytometry, culture systems, and related tools used worldwide to empower biomedical discovery and translational applications.

Illumina
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: American company incorporated that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California.

Agilent Technologies
type: NamedIndividual
type: Concept
broader: LC instrument vendor
broader: LC column vendor
definition: Company provides laboratories worldwide with analytical instruments and supplies, clinical and diagnostic testing services, consumables, applications and expertise in life sciences and applied chemical markets.

Illumina NextSeq 500 System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: High-throughput sequencing machine which enables sequencing of exomes, whole genomes, and transcriptomes. It also provides flow cell types, real-time analysis, and integration with Illumina's BaseSpace computing environment.
preferred label: NextSeq 500

Illumina NextSeq 550 System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: The NextSeq 550 System brings the power of a high-throughput sequencing system to your benchtop. With tunable output and high data quality, it provides the flexible power you need for whole-genome, transcriptome, and targeted resequencing.
preferred label: NextSeq 550

Illumina HiSeq 2500 System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world.
preferred label: HiSeq 2500

Illumina HiSeq 3000/HiSeq 4000 System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Sequencer that uses patterned flow cell technology to provide high-performance sequencing. Perform production-scale, high-throughput exome or transcriptome sequencing projects quickly and economically.
preferred label: HiSeq 4000

Illumina NovaSeq 6000 System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: System unleashes groundbreaking innovations that leverage our proven technology. Now you can get scalable throughput and flexibility for virtually any sequencing method, genome, and scale of project.
preferred label: NovaSeq 6000

Hamamatsu Photonics
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: Preparation instrument vendor
definition: Manufacturer of optical sensors including, photomultiplier tubes, electric light sources, and other optical devices and their applied instruments for scientific, technical and medical use.
preferred label: Hamamatsu

Keyence BZ-X710 fluorescent microscope
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: All in one fluorescence microscope BZ-X710 by Keyence, Japan.
preferred label: BZ-X710

Bruker Corporation
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: LC instrument vendor
broader: LC column vendor
definition: Commercial organization located in Massachusetts, USA, for scientific instruments and analytical and diagnostic solutions. Bruker equipment can be used in life science molecular research, in applied and pharma applications,microscopy, nano-analysis and industrial applications. Provider of high-performance systems for cell biology, preclinical imaging, clinical phenomics and proteomics research, clinical microbiology, and for molecular pathology research.
preferred label: Bruker

Zeiss LSM 710 Confocal Inverted Microscope
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Inverted microscope that enables confocal microscopy in cell and developmental biology.
preferred label: LSM 710 Confocal Microscope

10x Genomics Chromium Plus Genetic Analyzer
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Genetic analyzer, referred to as Chromium Controller for combining large partition numbers with a diverse barcode library to generate >100,000 barcode-containing partitions.
preferred label: Chromium Controller

Fluidigm CyTOF Helios mass cytometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Mass cytometer that enables deep profiling of translational and clinical research samples across range of cell surface and intracellular markers.
preferred label: Helios

Sciex QTRAP 5500 mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: QTRAP 5500 system Performs multiple reaction monitoring (MRM) for quantitation using this high-sensitivity triple quadrupole system. Identify, characterize, and quantitate metabolites more quickly and easily.Discover and quantitate targeted biomarkers. Enable high-sensitivity full-scan MS, MS/MS, and MS3 with high-selectivity from true triple quadrupole precursor ion (PI) and neutral loss (NL) scans.
preferred label: QTRAP 5500

Thermo Scientific Q Exactive HF Hybrid Quadrupole-Orbitrap mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Identify and quantify more proteins, peptides, lipids, glycans and small molecules accurately and in less time with the Thermo Scientific Q Exactive HF hybrid quadrupole-Orbitrap mass spectrometer. The Q Exactive HF system combines a state-of-the-art segmented quadrupole for high-performance precursor ion selection with a high-resolution, accurate-mass (HR/AM) ultra-high-field Orbitrap mass analyzer to deliver a superior combination of scan speed, resolving power, mass accuracy, spectral quality and sensitivity. Identify, quantify and confirm in a single analysis with a single instrument with the Q Exactive HF mass spectrometer.
preferred label: Q Exactive HF

Thermo Scientific Orbitrap Fusion Tribrid mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Thermo Orbitrap Fusion Tribrid mass spectrometer and Waters M-Class Acquity nanoUPLC is a versatile platform. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments.
preferred label: Orbitrap Fusion Tribrid

Thermo Scientific Orbitrap Fusion Lumos Tribrid mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Spectrometer performs analysis including low level PTM analysis, multiplexed relative quantitation using isobaric tags, intact protein characterization, and MSn analysis of small molecules. System incorporates the brightest ion source, segmented quadrupole mass filter with improved selectivity and ion transmission, Advanced Vacuum Technology, and ETD HD.
preferred label: Orbitrap Fusion Lumos Tribrid

Thermo Scientific Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass Spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Uses high capacity transfer tube for maximum ion loading, electrodynamic ion funnel that accomodates and transmits ions over broad mass range. These components enable identification and analysis of peptides, label free and TMT quantitation, top down proteomics analyses, sophisticated DDA and DIA, dynamic Retention Time PRM and BioPharma characterization.
preferred label: Q Exactive HF-X

Thermo Scientific Q Exactive GC Orbitrap mass spectrometry
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Identify, quantify and confirm more compounds rapidly and with confidence using the Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer. This benchtop LC-MS/MS system combines quadruple precursor ion selection with high-resolution, accurate-mass (HRAM) Orbitrap detection to deliver performance and versatility. The Q Exactive Mass Spectrometer is equally useful for untargeted or targeted screening and a broad range of qualitative and quantitative applications in drug discovery, proteomics, environmental and food safety, clinical research and forensic toxicology.
preferred label: Q Exactive

Thermo Scientific Q Exactive UHMR Hybrid Quadrupole-Orbitrap Mass Spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Perform the highest - quality native intact mass and top-down analysis in structural biology and biopharma research. The Thermo Scientific Q Exactive UHMR (Ultra-High Mass Range) Hybrid Quadrupole-Orbitrap Mass Spectrometer is the first UHMR MS to combine substantially increased sensitivity and mass resolution at high m/z, MS2, and psuedo-MS3 capabilities in a single platform.
preferred label: Q Exactive UHMR

Zeiss Lightsheet Z.1 fluorescence microscope
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Light sheet fluorescence microscope for the imaging of large cleared specimens. Lightsheet Z.1 with Clr Plan-Apochromat 20x/1.0 Corr nd=1.38 is used to perform experiments with tissue cleared by Scale medium (Hama et al, Nat Neurosci. 2011), which has a refractive index of n=1.38.
preferred label: Zeiss LightSheet Z.1

Zeiss Axio Scan.Z1 Slide Scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Digitize your specimens with the Axio Scan.Z1 slide scanner and create high-quality virtual slides. Axio Scan.Z1 tackles the most demanding virtual microscopy research tasks as easily as it handles your routine work. The software module ZEN slidescan is designed specifically for the workflow of capturing virtual slides, while ZEN image analysis tools prepare your data accurately. Organize your virtual slides with ZEN browser, the web-based database, then view your data from any location using any operating system , or share virtual microscopy images online with colleagues and organize your projects, even when you are on the go.
preferred label: Axio Scan.Z1

Leica Aperio AT2 Scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Digital whole slide scanner.400 slide capacity brightfield scanner. High throughput with small footprint. 2x3 slide option available.Aperio AT2 runs on Microsoft Windows 10 operating system.
preferred label: Aperio AT2

Hamamatsu NanoZoomer 2.0-HT Digital slide scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: High speed, high resolution digital scanner with network features. User friendly full slide scanner designed to process up to 210 slides automatically.
preferred label: NanoZoomer 2.0-HT

NanoString GeoMx Digital Spatial Profiler
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Integrated commercial system comprising hardware, software and nCounter chemistry that enables simultaneous, highly multiplex spatial profiling of proteins or RNA in FFPE tissues. DSP platform quantifies abundance of protein or RNA by counting unique indexing oligonucleotides assigned to each target of interest. Used to rapidly and quantitatively assess biological implications of heterogeneity within tissue samples.
preferred label: Digital Spatial Profiler

Biomark HD system
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Automated, high performance PCR/qPCR system that uses microfluidics technology to process samples at nanoliter scale volumes for gene expression, genotyping, sample identification, copy number variation analysis and digital PCR. With wide range of integrated fluidic circuit (IFC) formats available, scaling from mid to high throughput on single system.
preferred label: Biomark HD

Hyperion Imaging System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Imaging system enables comprehensive analysis of cellular phenotypes. Allows access to single cell insights. This includes deeper understanding of intricate spatial relationships of cells, pathways and phenotypes in tissue microenvironment.

PhenoImager Fusion
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Brightfield and fluorescent whole slide imager with Multispectral Imaging Technology.

Cytiva
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Cytiva is the new name of the former GE Healthcare Life Sciences biopharma business following its acquisition by Danaher Corporation, according to an April 1, 2020 announcement. Provider of life sciences brands such as ÄKTA, Amersham, HyClone, MabSelect and Whatman.

Leica Biosystems
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: Preparation instrument vendor
definition: Medical devices company that develops and supplies clinical diagnostics to pathology market. It is also research, instrument, and medical device company as well as division of Danaher Corporation with headquarters Wetzlar, Germany.

Keyence
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Direct sales organization that develops and manufactures automation sensors, vision systems, barcode readers, laser markers, measuring instruments, and digital microscopes. Founder Takemitsu Takizaki. Headquarters Osaka, Osaka, Japan.

Ionpath
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: Preparation instrument vendor
definition: Pioneer in high definition spatial proteomics, tissue imaging and analysis to accelerate medical discovery and improve human health. With MIBI technology and expertise of pathology and data science teams, Ionpath provides actionable insights to translational and clinical researchers at leading pharmaceutical, biotechnology, and research organizations in immuno-oncology, immunology, neuroscience, and infectious disease research.

Standard BioTools
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: American company engaged in design, manufacture and sale of biological research equipment based on integrated fluidic circuit technology. Founders leveraged their semiconductor experience to create integrated circuits that carried fluids rather than electrons.
preferred label: Standard BioTools (Fluidigm)

Zeiss Microscopy
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Manufacturer of light, electron, X-ray and ion microscope systems. Offers solutions for correlative microscopy. Provides products and services for life sciences, materials and industrial research, as well as education and clinical practice.

Andor
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Provides development and manufacture of high performance scientific digital cameras, microscopy systems and spectrographs for academic, industrial and government applications.

Andor Zyla 4.2 sCMOS
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Zyla 4.2 PLUS is the latest sCMOS technology advancement from Andor. At its heart, Zyla 4.2 PLUS benefits from latest generation sCMOS sensor technology, delivering a further 10 % boost in QE, resulting in an unprecedented 82% QEmax.
preferred label: Zyla 4.2 sCMOS

Leica SCN400 slide scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Provides fully digitized image of speciment that can be viewed and edited from virtually anywhere.
preferred label: SCN400

Ionpath MIBIscope System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Imaging platform, enabling phenotypic profiling and spatial analysis of tissue microenvironment. Enables over 40 markers to be visualized simultaneously with single step staining and single step imaging.
preferred label: MIBIscope

Illumina NextSeq 2000 System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Sequencing system supports range of methods such as exome sequencing, target enrichment, single-cell profiling.
preferred label: NextSeq 2000

Bruker timsTOF fleX with MALDI-2
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Instrument for probing molecular content of sample with MALDI-2. The timsTOF fleX is fully functional high speed, high sensitivity ESI instrument for all X-Omics analyses, combined with high spatial resolution MALDI source and stage specifically designed for resolving molecular distributions and bringing spatial dimension to OMICS analyses.
preferred label: timsTOF FleX MALDI-2

GE Healthcare IN Cell Analyzer 2200
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Cell imaging system for fast, automated imaging in fixed and live cells. Instrument can rapidly image cells using laser autofocusing, LED light source and CMOS camera.
preferred label: IN Cell Analyzer 2200

Keyence BZ-X800 fluorescent microscope
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Automated high-resolution microscope for Life Science research.
preferred label: BZ-X800

Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Mass spectrometer designed for most difficult analytical challenges. Incorporates inventions in ion transmission and control, extended m/z range, and real-time decision making. System suited for proteomics, structural biology, small-molecule, and biopharmaceutical characterization experiments.
preferred label: Orbitrap Eclipse Tribrid

Sciex
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: LC instrument vendor
definition: Manufacturer of mass spectrometry instrumentation used in biomedical and environmental applications. Originally started by scientists from the University of Toronto Institute for Aerospace Studies, it is now part of Danaher Corporation with the SCIEX R&D division still located in Toronto, Canada.

10x Genomics
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: Preparation instrument vendor
definition: American biotechnology company that designs and manufactures gene sequencing technology used in scientific research.

Zeiss Axio Observer 5
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Inverted microscope Axio Observer 5 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging.
preferred label: Axio Observer 5

Zeiss Axio Observer 3
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Inverted microscope Axio Observer 3 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging.
preferred label: Axio Observer 3

Zeiss Axio Observer 7
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Inverted microscope Axio Observer 7 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging.
preferred label: Axio Observer 7

HTX Sublimator
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Automated MALDI matrix deposition system offering speed, reproducibility, and smallest available crystals for sub-micron resolution mass spectrometry imaging. Features rectangular vacuum chamber that achieve sublimation conditions extremely quickly to maximize efficiency for imaging MS sample preparation.
preferred label: Sublimator

HTX M3+ Sprayer
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Sample preparation platform offering automated advanced MALDI matrix sprayer.
preferred label: M3+ Sprayer

HTX TM-Sprayer
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Allows users to adjust both gas flow rate and nozzle velocity to control drying time, preventing analyte delocalization and formation of large matrix crystals, known to create hot spots on MALDI images. Allows to heat matrix solution as it is being applied to their sample. By increasing temperature of matrix solution, absorption of matrix into sample is increased, resulting in greater MALDI image resolution.
preferred label: TM-Sprayer

HTX M5 Sprayer
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Sprayer builds on capabilities of HTX TM-Sprayer providing innovative M5 chassis, high velocity stage and heated sample holder drawer. Sample plate holder is mounted on drawer mechanism to allow easy loading of samples, better protection of user and better alignment of various plate types. New High-Velocity XY stage allows nozzle displacement speed of up to 5,600mm/min and expands process range. Super dry spray can be achieved at high flow rates of solvent further improving instrument performance. E/Z trough gutter design improves chemical containement and is easy to remove and clean. Bulkhead connectors are directly mounted on it to also allow easy access to in line filter.
preferred label: M5 Sprayer

HTX Technologies
type: NamedIndividual
type: Concept
broader: Preparation instrument vendor
definition: Company offers sample preparation solutions for Mass Spectrometry Imaging. HTX delivers customized solutions for sample preparation and workflow automation of advanced analytical platforms.

Hamamatsu NanoZoomer S210 Digital slide scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
broader: Preparation instrument model
definition: NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S210 provides high performance capable of handling large number of slides.
preferred label: NanoZoomer S210

Hamamatsu NanoZoomer S360 Digital slide scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
broader: Preparation instrument model
definition: NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S360 is ideal for use in hospitals and clinical laboratories.
preferred label: NanoZoomer S360

Hamamatsu NanoZoomer S60 Digital slide scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
broader: Preparation instrument model
definition: NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S60 supports brightfield imaging, fluorescence imaging and double size slides.
preferred label: NanoZoomer S60

Hamamatsu NanoZoomer-SQ Digital slide scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: NanoZoomer is a family of whole slide scanners that convert glass slides into high resolution digital data by high speed scanning. Desktop single slide compact scanner for creating whole slide images of single tissue slides.
preferred label: NanoZoomer-SQ

Phenocycler-Fusion
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: PhenoCycler-Fusion system is integrated platform combining automated, ultrahigh-plex cycling platform, Akoya PhenoCycler, and its high-speed imaging platform, PhenoImager (formerly Phenoptics), into end-to-end, integrated workflow.
preferred label: Phenocycler-Fusion 2.0

Akoya Biosciences
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: Preparation instrument vendor
definition: Spatial biology company offering solutions for high parameter tissue analysis from discovery through clinical and translational research, enabling development of more precise therapies for immuno-oncology and other drug development applications.

SunCollect MALDI Sprayer
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: For tissue preparation for Imaging MALDI. The sprayer can handle fresh-frozen or FFPE tissue sections. Enzymes such as trypsin can be applied to the tissue for in situ digestion. Sprayer offers the following key features: Automated delivery of matrix, enzyme or derivatization solutions; 6 port PEEK valve with low dead-volume to minimise liquid usage; Automatic self-cleaning function at end of matrix application; 100 % biocompatible; Compact unit 36 x 49 x 40 cm (w,d,h);Preprogrammed spray protocols;Up to 8 sample slides can be sprayed simultaneously;Easy to use software.
preferred label: SunCollect Sprayer

SunChrom
type: NamedIndividual
type: Concept
broader: Preparation instrument vendor
definition: Develops and manufactures scientific instruments. Specialists for system solutions in liquid chromatography, development and optimization of front-end applications and sample preparation systems for MALDI and MALDI-MSI.

nanoString CosMx Spatial Molecular Imager
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Integrated system with mature cyclic fluorescent in situ hybridization chemistry, resolution imaging readout, interactive data analysis and visualization software. Analysis platform to provide spatial multiomics with formalin-fixed paraffin-embedded and fresh frozen tissue samples at cellular and subcellular resolution. CosMx SMI enables rapid quantification and visualization of up to 1,000 RNA and 64 validated protein analytes. Spatial single-cell imaging platform that drives deeper insights for cell atlasing, tissue phenotyping, cell-cell interactions, cellular processes, and biomarker discovery.
preferred label: CosMx Spatial Molecular Imager

10x Genomics Xenium Analyzer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Xenium Analyzer offers subcellular profiling of 100s to 1,000s of RNA targets alongside multiplexed protein, in fresh, frozen or FFPE tissue.
preferred label: Xenium Analyzer

Resolve Biosciences
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Biotechnology research company for molecular cartography. Applys the power of Molecular Cartography to enable scientists to gain new insights based on the highest-resolution view of single-cell spatial biology.

NanoString Technology
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Publicly held biotech company offering discovery and translational research solutions. NanoString's products include the nCounter® Gene Expression System, the GeoMx® Digital Spatial Profiler, the CosMx™ Spatial Molecular Imager, and the AtoMx™ Spatial Informatics Platform.
preferred label: NanoString

Leica Autostainer ST5010 XL
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Leica ST5010 Autostainer XL provides reproducible, consistent high quality staining, and increased workload throughput compared to manual staining.
preferred label: AutoStainer XL

Zeiss Lightsheet 7
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: System for imaging of living and cleared specimens. Used to image large optically cleared specimens in toto with subcellular resolution. Dedicated optics, sample chambers and holders allow adaption to the refractive index of your chosen clearing method.
preferred label: Lightsheet 7

Resolve Biosciences Molecular Cartography
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Platform is multi-analyte, multiplex spatial analysis technology that enables scientists to resolve complex biological challenges in areas such as oncology, neuroscience, and infectious disease. Platform produces contextual data sets that illuminate molecular interactions at subcellular resolution, while preserving the sample tissue.

10x Genomics Chromium iX Single Cell Analyzer
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Chromium iX offers cost effective, lower throughput single cell analysis, and can be upgraded to the high throughput full-range Chromium X.Chromium iX does not run high-throughput (HT) assays.
preferred label: Chromium iX

10x Genomics Chromium X Single Cell Analyzer
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Analyzer used for high throughput full range single cell analysis. Chromium X runs high-throughput assays. It runs all single cell assays, including high-throughput assays for Single Cell Immune Profiling and Single Cell Gene Expression.
preferred label: Chromium X

Illumina NovaSeq X Plus
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: NovaSeq X Plus Sequencing System has ability to sequence more than 128 genomes per run. Provides faster run times, and the ability to process data directly on the instrument. Uses dual flow cells. Production scale sequencing system can also perform broad range of data intensive applications, from single-cell analysis to exome and circulating tumor DNA sequencing.
preferred label: NovaSeq X Plus

Illumina NovaSeq X
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Updated NovaSeq to NovaSeq X. NovaSeq X Sequencing System achieves lower cost per genome by packing more genomes per flowcell, and that is because each flowcell has more wells for more fragments. NovaSeq X uses single flow cell.
preferred label: NovaSeq X

Visium CytAssist
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Compact, benchtop instrument that enables transfer of transcriptomic probes from standard glass slides to Visium slides, enabling spatial profiling insights to be gained from even more samples. Enables whole transcriptomic spatial profiling insights across entire tissue section, and expanded compatibility with FFPE and/or FF samples.

Waters
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: LC instrument vendor
broader: LC column vendor
definition: Publicly traded analytical laboratory instrument and software company headquartered in Milford, Massachusetts. Leading provider of lab equipment, supplies and software. Has pioneered chromatography, mass spectrometry, and thermal analysis innovations.

Evosep
type: NamedIndividual
type: Concept
broader: LC instrument vendor
broader: LC column vendor
definition: Business Services and Biotechnology Research company in Odense, Denmark.

IonOpticks
type: NamedIndividual
type: Concept
broader: LC column vendor
definition: Innovative Australian company that develops, manufactures and distributes advanced proteomics tools. Produces high performance nanoflow chromatography solutions for global research community.

Leica STELLARIS 5 microscope
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: STELLARIS 5 microscope has core system with integrated WLL, combined with proprietary Acousto-Optical Beam Splitter and Power HyD S detectors. Together with the TauSense technology, STELLARIS 5 sets a new standard for the quality of images and quantity of information generated. Imaging with user interface, ImageCompass.
preferred label: STELLARIS 5

Evident
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Company for development, manufacture, sale and provision of solutions for biological microscopes, industrial microscopes, industrial endoscopes, non-destructive inspection equipment, X-ray analyzers, etc.
preferred label: Evident Scientific (Olympus)

Olympus VS200 Slide Scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Flexible system that supports various slide sizes, different objectives, SILA optical sectioning device, oil dispenser, cameras, loaders, and LED/laser light sources with multiple filter sets. VS200 supports brightfield, darkfield, polarization, phase contrast, and fluorescence, with possibility to scan sample using multiple techniques at the same time. VS200 software supports offline analysis, deep learning, 3D deconvolution, and batch conversion to standard file formats. It also supports the NIS-SQL database for data management and the DICOM format for easy integration into lab information management system.
preferred label: VS200 Slide Scanner

3DHISTECH Pannoramic MIDI II Scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Automatic digital slide scanner with 12 slide capacity in one run, fluorescence scanning, 9 physical filter cubes and 45 logical fluorescence channels. Powered by PANNORAMIC Scanner Software. Supports Carl Zeiss objectives, achieving up to 43x or 86x magnification and 0.087 µm/pixel resolution within the same instrument, along with advanced FISH scanning technique.
preferred label: Pannoramic MIDI II Digital Scanner

MGI DNBSEQ-T7 Genetic Sequencer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Instrument features include High Speed: 22 hrs to 24 hrs for PE150 sequencing; High Flexibility: 4 Flow Cells, PE150, and PE100 at the same time; Ultra-high Throughput: 7 Tb per day; high quality data around the clock.
preferred label: DNBSEQ-T7

BGI Genomics
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Provider of precision medicine serving customers in more than 100 countries, involving over 2,300 medical institutions. Relying on sequencing and bioinformatics technology, provides clinical molecular diagnostic solutions and high-throughput sequencing research services.

MoticEasyScan One
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Compact scanner for any digital slide application. This scanning system with FS-Live software suite, optimized for frozen section, cytology, ROSE, and FNA adequacy evaluation, for remote pathologist to pilot the system and provide diagnosis without travel time.

Motic
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Company provides innovative microscope and microscopy solutions designed for education, medical, clinical, and industrial needs. Motic Microscopes specializes in designing and manufacturing conventional and digital microscopy solutions. Motic Digital Pathology drives adoption of digital medicine by making whole slide imaging, AI, and software technologies approachable for hospitals and labs everywhere.Motic Electric designs, develops and manufactures High Voltage insulation components for transmission and distribution systems in the electric power industry.Motic Energy strives to lead in smart energy technology through our next-gen management platform, using big data, AI, and cloud technology to create networked energy ecosystem for the world.

Leica DM6 B Upright Microscope
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Leica DM6 B Upright Microscope includes the Leica DFC7000 T Camera and LAS X Software.
preferred label: DM6 B

TissueScope LE Slide Scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Scanner for versatility, throughput, and ease of use. Scan up to twelve 1” x 3” brightfield slides, up to six 2” x 3” slides, or any size slide up to 6”x 8”.

Huron Digital Pathology
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Manufacturer in St. Jacobs, Ontario, Canada. Provides whole slide scanners to clinical and research institutions. Offers slide scanning services. Each customer is given secured access to view and download their images. After scanning is complete, the glass specimens are returned if requested by the customer.

Leica ST5020 Multistainer Slide Stainer
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Histology multistainer produces results for both routine and special stains and can perform single or multiple protocols at the same time. Contains 12 slide racks and 34 reagent stations.
preferred label: ST5020 Multistainer

EVOS M7000 Imaging System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
broader: Preparation instrument model
definition: Fully automated, inverted, multi-channel fluorescence and transmitted light imaging system. System with acquisition tools with enhanced autofocus algorithms and automated routines for microwell plate assays, time-lapse live cell imaging, area scanning in time lapse and Z-stacks in scan mode to generate publication quality images and data.
preferred label: EVOS M7000

Roche Diagnostics
type: NamedIndividual
type: Concept
broader: Preparation instrument vendor
definition: Roche Diagnostics develops and produces medical tests and digital tools that provide information to help healthcare professionals find the right treatment for patients and deliver the best patient care to improve, prolong and save lives.

Ventana Discovery Ultra
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: Automated slide preparation system to run manual and fully automated experiments simultaneously with no synchronization errors. Ability to fully automate broad range of IHC and ISH assays, including FISH, gene and protein IHC/ISH, mRNA ISH and multiplex assays with any combination of IHC and ISH. Automated baking, deparaffinization, cell conditioning and staining including immunohistochemistry (IHC) and in situ hybridization (ISH) Enhanced multiplexing and immunofluorescence, 30 slide reaction chambers allow for independent protocols for each individual slide. Ready-to-use optimized reagents.
preferred label: Discovery Ultra

Leica Aperio CS2 Scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Image capture brightfield whole slide scanner for low throughput with five slide capacity and 20X and 40x magnification capabilities. 2x3 slide option available for large slides. Aperio CS2 runs on Microsoft Windows 10 operating system.
preferred label: Aperio CS2

10x Genomics Chromium Connect system
type: NamedIndividual
type: Concept
broader: Preparation instrument model
definition: System that combines proprietary 10x microfluidics technology using Chromium Automated Controller with precise, automated liquid handling that allows users to run 10x Genomics end to end library construction workflow with minimal user interaction. Integrates components customized for 10x Genomics single cell workflows, automation specific reagents and consumables, and touchscreen computer. Used to generate consistent and reproducible single cell gene expression results across experiments, users, and multiple sites.
preferred label: Chromium Connect

Keyence BZ-X810 microscope
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Inverted fluorescence phase contrast microscope. Objective lenses. BZ Series infinite optical system.
preferred label: BZ-X810

Discovery MR750 3.0T MR system
type: NamedIndividual
type: Concept
broader: Imaging instrument model
definition: Whole body magnetic resonance imaging scanner designed to support high resolution, high signal-to-noise ratio and fast scan times. This MRI system features superconducting magnet that operates at 3. O Tesla.
preferred label: Discovery MR750

GE HealthCare
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
broader: Imaging instrument vendor
definition: Provides digital infrastructure, data analytics and decision support tools to help in diagnosis, treatment and monitoring of patients.
preferred label: GE Healthcare

Shimadzu
type: NamedIndividual
type: Concept
broader: LC instrument vendor
definition: Leading-edge science and technologies in analytical and measuring instruments including chromatographs and mass spectrometry. Manufactures precision instruments, measuring instruments and medical equipment.

Vizgen MERSCOPE Ultra
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: System automates sample imaging, imaging analysis, and cell segmentation, delivering high-resolution, high-throughput imaging without compromising sensitivity. Powered by MERFISH technology, MERSCOPE Ultra includes high-performance analysis computer, along with the necessary reagents and software to accurately quantify and localize RNA and protein in tissue samples. High-resolution in situ spatial genomics platform that offers tissue-wide view of up to 1000 custom genes at single-cell resolution.
preferred label: MERSCOPE Ultra

Vizgen
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Biotechnology company in Cambridge, Massachusetts, developing the next generation of genomic profiling tools that enable researchers to gain new insight into the biological systems that underlie human health and disease with spatial context. The company's MERSCOPE platform enables massively multiplexed, genome-scale nucleic acid imaging with high accuracy and unrivaled detection efficiency at subcellular resolution.

Standard Biotools CyTOF XT mass cytometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Fully automated and affordable cytometer to simplify and standardize deep single-cell profiling studies.
preferred label: CyTOF XT

Element AVITI24 system
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Element AVITI24 system is the benchtop platform enabling high-quality, low-cost sequencing and single cell multiomics in one powerful system.
preferred label: AVITI

Element Biosciences
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Biotechnology company in San Diego, California focused on developing disruptive DNA sequencing and other omics technology for research markets.

Bruker timsTOF Ultra mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Mass spectrometer used for proteomics research. Offers the ultimate fusion of trapped ion mobility spectrometry (TIMS) with quadrupole time-of-flight (QTOF) technology.
preferred label: timsTOF Ultra

Bruker timsTOF Ultra 2 mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Spectrometer timsTOF Ultra 2 is paired with CaptiveSpray Ultra 2 ion source for high sensitivity to work with challenging samples and detect low-abundance peptides. Used to analyze even the smallest amounts and uncover previously unseen peptides.
preferred label: timsTOF Ultra 2

Bruker timsTOF SCP mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: The timsTOF SCP (single-cell proteomics) is mass spectrometer from Bruker. Ultra-high sensitivity instrument for quantitative single cell biology research with unbiased, deep single-cell 4D-Proteomics, immunopeptidomics, epiproteomics and PTM analysis. It features an additional separation in the tims cell where ions get separated according to their ion mobility, leading to collision cross-section values.Allows the analysis of hundreds of samples with minimal sample load (<200 ng) at sequencing speeds exceeding 100 Hz.
preferred label: timsTOF SCP

Bruker timsTOF HT mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Mass spectrometer is equipped with the 4th generation high capacity TIMS-XR analyzer and advanced digitizer technology (ADT). Offers higher dynamic range for unmatched analytical depth and quantitation in high-throughput proteomics experiments.
preferred label: timsTOF HT

Bruker timsTOF Pro mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Mass spectrometry (MS)-based proteomics instrument designed for shotgun proteomics and phosphoproteomics, leveraging Parallel Accumulation Serial Fragmentation (PASEF) technology to enhance speed, sensitivity, and resolution.
preferred label: timsTOF Pro

Bruker timsTOF Pro 2 mass spectrometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Mass spectrometer used for research, particularly in proteomics and metabolomics, leveraging Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation Serial Fragmentation (PASEF) technologies for enhanced 4D-omics capabilities.
preferred label: timsTOF Pro 2

Fluidigm CyTOF 2 mass cytometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Time-of-Flight mass spectrometer for high-speed acquisition of highly multi-parametric single cell data. Simultaneously resolves multiple parameters with minimal signal overlap, providing insights into the functional and phenotypic complexity of biological systems at the single-cell level. Analyzes cells labeled with panel of reagents conjugated to stable metal isotopes using time-of-flight mass cytometry technology. Includes over 120 detection channels and 35 Maxpar metal probes.
preferred label: CyTOF 2

Leica DMi8 Inverted Microscope
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Leica DMi8 microscope is an inverted light microscope, intended as a general microscope for routine examinations of biological specimens.
preferred label: DMi8

Singular Genomics
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Publicly-traded life science technology company, which specializes in advanced next-generation sequencing (NGS) and multiomic technologies.

Singular Genomics G4X Spatial Sequencer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Ultra high-throughput, spatial sequencing platform, for integrated multiomic analysis of FFPE samples at subcellular resolution. Spatial sequencing platform capable of simultaneous direct RNA.
preferred label: G4X Spatial Sequencer

Bruker timsTOF FleX
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: The timsTOF fleX is fully functional high speed, high sensitivity ElectroSpray Ionization (ESI) instrument for all Omics analyses with integrated Matrix-Assisted Laser Desorption Ionization (MALDI) source for fast MALDI Imaging.
preferred label: timsTOF FleX

Complete Genomics
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Biotechnology company that has developed and commercialized DNA sequencing platform for human genome sequencing and analysis. The company is a wholly-owned subsidiary of MGI.

3DHISTECH
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: European company specializing in digital pathology. Based in Budapest, Hungary, they develop high-performance slide scanners and software tools that digitize and streamline pathology workflows for diagnostics, research, and education.

Cytek Biosciences
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Leading manufacturer and supplier of flow cytometry products and services. Cytek’s compact, affordable instruments and wide ranging support offerings are used by researchers and clinicians all over the world.

Cytek Northern Lights flow cytometer
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Flow cytometer, with its easy-to-use workflow, is full spectrum flow cytometry solution. Instrument incorporates Cytek’s Full Spectrum Profiling technology allowing for wide array of new fluorochrome combinations without reconfiguring your system for each application. Uses SpectroFlo software.The 1-Laser, 2-Laser, and 3-Laser versions of this model are available.
preferred label: Cytek Northern Lights

Zeiss Axio Zoom.V16 for Biology
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: ZEISS Axio Zoom.V16 microscope system includes fluorescence zoom microscope for large fields. Designed for brightfield and fluorescence microscopy of biological samples. Microscope design is optimized for fluorescence microscopy with specific optical components for light management involving specialized filters and dichroic mirrors.
preferred label: Axio Zoom.V16

Microscopes International
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: Microscopes International (often branded as “uScope” by Microscopes International) is a Plano, Texas–based company (est. 2009) specializing in affordable, highly portable digital microscopes and whole‑slide scanning systems for scientific, clinical, and field applications.

Bruker solariX
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Bruker solariX is magnetic resonance mass spectrometry (MRMS) platform, available with high-field magnets ranging from 7 T up to 15 T.
preferred label: solariX

Microscopes International uScopeHXII-20 microscope
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Compact, high-resolution digital microscope and whole slide scanner designed for professionals in fields like pathology, histology, and research. It features 20x Infinity Plan Apochromatic objective with 0.65 numerical aperture, offering balance between magnification and depth of field—ideal for imaging thicker tissue sections and smears with enhanced clarity.
preferred label: uScopeHXII-20

Fluidigm Juno Targeted DNA Sequencing Library Preparation System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Juno system used for preparing libraries for next-generation sequencing and IFS preparation for gene expression, genotyping and digital PCR application.
preferred label: Juno System

Leica Cell DIVE Multiplex Imaging Solution System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Cell DIVE Multiplex Imaging Solution is Leica Microsystems’ open, highly customizable platform that combines precision-engineered hardware, iterative staining/dye‑inactivation protocols, and intuitive software to visualize 60+ biomarkers from a single tissue section—delivering crystal-clear, whole‑tissue imaging at the single‑cell level.
preferred label: Cell DIVE

3DHISTECH Pannoramic 150 Digital Scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: The Pannoramic 150 is a versatile digital pathology system designed for high-speed, high-resolution brightfield and fluorescence scanning. Equipped with a continuously moving stage, advanced Plan-Apochromat optics including a 10x objective, and a back-illuminated sCMOS camera, it delivers exceptional image clarity and efficiency for research applications.
preferred label: Panoramic 150 Digital Scanner

Revvity Inc.
type: NamedIndividual
type: Concept
broader: Acquisition instrument vendor
definition: American company in the life sciences and diagnostics business that is focused on selling to the pharmaceutical and biotechnology industries, especially in relation to approaches making use of new cell therapy or gene therapy developments.
preferred label: Revvity

Revvity Opera Phenix Plus High Content Screening system
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Imaging system is confocal imaging platform designed for high-throughput biological assays. Supports phenotypic screening and imaging of complex biological models, including live cells, primary cells, and microtissues.
preferred label: Opera Phenix Plus HCS

Waters SYNAPT G2-Si mass spectrometry system
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: High-resolution mass spectrometer with ion mobility, designed for deep, accurate analysis of complex samples across life science and analytical chemistry research. System adds Ion Mobility Separation to the original SYNAPT G2's high-resolution QuanTof technology, offering a third dimension of separation (size/shape) for superior selectivity, sensitivity, and structural insight in complex samples, beyond just mass and chromatography. The G2-Si integrates StepWave optics and enhanced data workflows for better performance in proteomics, metabolomics, and biomarker discovery.
preferred label: SYNAPT G2-Si

PerkinElmer Opera Phenix High Content Screening System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: A fully automated, high-content imaging and analysis platform designed for high-throughput biological screening and detailed cellular phenotyping. It’s widely used in research settings for applications that require both high resolution and high throughput microscopy across a range of complex biological models.
preferred label: Opera Phenix HCS

Miltenyi Biotec MACSima System
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: Fully automated high-content imaging platform that uses cyclic immunofluorescence to enable high-plex spatial profiling of hundreds of protein markers and dozens of RNAs on the same tissue section, accelerating spatial biology and multiomics research workflows.
preferred label: MACSima System

Hamamatsu NanoZoomer 2.0-RS Digital slide scanner
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: The NanoZoomer 2.0-RS is a compact and cost-effective digital slide scanner. It maintains the performance of the NanoZoomer 2.0-HT, with the primary difference being the number of slides processed automatically. It can automatically process up to 6 standard slides (76 mm × 26 mm) or 2 double-size slides (76 mm × 52 mm).
preferred label: NanoZoomer 2.0-RS

Regressive staining
type: NamedIndividual
type: Concept
broader: Stain technique
definition: A staining technique that involves over-staining the tissue initially and then removing excess stain with a decolorizing agent. This process allows for more selective staining of specific cell components or structures while reducing background staining. Eosin is an example of a regressive staining technique commonly used to stain the cytoplasm in histology. [Generated by an AI language model]

Stored in refrigerator
type: NamedIndividual
type: Concept
broader: Preparation condition
broader: Storage method
definition: A preservation method of sample specimens in a refrigerator which maintains temperatures around 4 degrees Celsius but not below 0 degress Celsius, as defined by NCIT, ensuring the specimens' stability without freezing.

MACS tissue storage solution
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium

Inflated (Agarose)
type: NamedIndividual
type: Concept
broader: Preparation medium

Frozen at -20 degrees celsius
type: NamedIndividual
type: Concept
broader: Preparation condition
broader: Storage method

Left-and-down
type: NamedIndividual
type: Concept
broader: Scan direction

Snake-by-columns
type: NamedIndividual
type: Concept
broader: Tile configuration

Left-and-up
type: NamedIndividual
type: Concept
broader: Scan direction

um^3
type: NamedIndividual
type: Concept
broader: Volume unit

Modified progressive staining
type: NamedIndividual
type: Concept
broader: Stain technique
definition: A variation of the traditional progressive staining technique used in histology and microscopy. In modified progressive staining, alterations are made to the staining procedure to achieve specific staining results or to highlight certain cellular components or structures more effectively. [Generated by an AI language model]

DMSO (no serum)
type: NamedIndividual
type: Concept
broader: Storage medium

Fixed frozen OCT (Formalin, sucrose protected)
type: NamedIndividual
type: Concept
broader: Preparation medium

Allprotect tissue reagent (ALL)
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium

Snake-by-rows
type: NamedIndividual
type: Concept
broader: Tile configuration

Inflated (OCT)
type: NamedIndividual
type: Concept
broader: Preparation medium

DMSO (serum)
type: NamedIndividual
type: Concept
broader: Storage medium

Fresh frozen OCT
type: NamedIndividual
type: Concept
broader: Preparation medium

Fresh frozen CMC
type: NamedIndividual
type: Concept
broader: Preparation medium

Endogenous fluorophore
type: NamedIndividual
type: Concept
broader: Analyte class
definition: Naturally occurring fluorescent molecules or compounds within biological samples or materials. These fluorophores emit light (fluoresce) when excited by specific wavelengths of light. They are a key component in various analytical techniques, particularly in fluorescence microscopy and spectroscopy, as they can be used to visualize and study biological structures and processes without the need for external labeling or staining. [Generated by an AI language model]

Frozen at -80 degrees celsius
type: NamedIndividual
type: Concept
broader: Storage method

Column-by-column
type: NamedIndividual
type: Concept
broader: Tile configuration

CLARITY hydrogel
type: NamedIndividual
type: Concept
broader: Preparation medium

Tris-EDTA
type: NamedIndividual
type: Concept
broader: Storage medium

mm^3
type: NamedIndividual
type: Concept
broader: Volume unit

Right-and-down
type: NamedIndividual
type: Concept
broader: Scan direction

Row-by-row
type: NamedIndividual
type: Concept
broader: Tile configuration

Bouin's
type: NamedIndividual
type: Concept
broader: Preparation medium

Right-and-up
type: NamedIndividual
type: Concept
broader: Scan direction

Progressive staining
type: NamedIndividual
type: Concept
broader: Stain technique
definition: A staining technique where the tissue or specimen is exposed to a staining solution for a specific period of time, and the staining intensity increases as staining progresses. This method is commonly used in routine histology to stain tissues for microscopic examination. Hematoxylin and eosin (H&E) staining is a classic example of a progressive staining method. [Generated by an AI language model]

Frozen on ice
type: NamedIndividual
type: Concept
broader: Preparation condition
broader: Storage method
definition: A sample that is in a frozen state maintained with ice.

Fixed frozen OCT (PFA, sucrose protected)
type: NamedIndividual
type: Concept
broader: Preparation medium

Incubated at 37 degrees celsius
type: NamedIndividual
type: Concept
broader: Preparation condition
broader: Storage method

Fixed frozen OCT (Cytofix/Cytoperm)
type: NamedIndividual
type: Concept
broader: Preparation medium

Miltenyi Tissue Preservation Buffer
type: NamedIndividual
type: Concept
broader: Perfusion solution
broader: Transport solution
definition: A specialized solution designed to preserve the viability and integrity of tissue samples and cells for extended periods, facilitating their use in various downstream applications such as cell separation and flow cytometry. [Generated by an AI language model]

University of Wisconsin Solution
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Perfusion solution
broader: Transport solution
definition: UWS stands for "University of Wisconsin Solution" and it is a cold storage solution designed to preserve organs for transplantation. It is commonly used for the preservation of organs such as the liver, kidney, and pancreas during the time between organ removal from the donor and transplantation into the recipient. [Generated by an AI language model]
preferred label: UW Solution
preferred label: UWS Solution

Histidine-Tryptophan-Ketoglutarate Solution
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Perfusion solution
broader: Transport solution
definition: HTK stands for "Histidine-Tryptophan-Ketoglutarate" solution. HTK solution is a type of cardioplegia solution used in cardiac surgery, particularly in heart transplantation and certain open-heart surgeries. [Generated by an AI language model]
preferred label: HTK Solution

Belzer MPS/KPS
type: NamedIndividual
type: Concept
broader: Perfusion solution
broader: Transport solution
definition: Belzer MPS (University of Wisconsin Machine Perfusion Solution) and Belzer KPS (University of Wisconsin Kidney Perfusion Solution) are specialized perfusion solutions used in the field of organ transplantation and preservation. These solutions are designed to protect and preserve organs, such as kidneys, during the time between removal from a donor and transplantation into a recipient. [Generated by an AI language model]

Saline (Buffered)
type: NamedIndividual
type: Concept
broader: Transport solution
definition: A solution that is used for preserving and transporting biological samples, particularly those that are sensitive to changes in pH. This type of solution typically contains saline, which is a solution of salt (usually sodium chloride) in water, along with a buffer system. [Generated by an AI language model]

Cell DIVE dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Cell DIVE assay.
preferred label: Cell DIVE

CODEX dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the CODEX assay.
preferred label: CODEX

Light Sheet dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Light Sheet assay.
preferred label: Light Sheet

MIBI dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Multiplex Ion Beam Imaging (MIBI) assay.
preferred label: MIBI

snATACseq dataset
type: NamedIndividual
type: Concept
broader: Dataset type (SenNet)
definition: Dataset generated from performing the snATAC-seq assay.
preferred label: snATACseq

snRNAseq dataset
type: NamedIndividual
type: Concept
broader: Dataset type (SenNet)
definition: Dataset generated from performing the snRNA-seq assay.
preferred label: snRNAseq

Visium dataset
type: NamedIndividual
type: Concept
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Visium assay.
preferred label: Visium

LC-MS dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the LC-MS assay.
preferred label: LC-MS

HiFi-Slide dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the HiFi-Slide assay.
preferred label: HiFi-Slide

Histology dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Histology assay.
preferred label: Histology

Fresh frozen gelatin
type: NamedIndividual
type: Concept
broader: Preparation medium

PhenoCycler dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the PhenoCycler assay.
preferred label: PhenoCycler

CyCIF dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the CyCIF assay.
preferred label: CyCIF

MALDI dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the MALDI assay.
preferred label: MALDI

SIMS dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the SIMS assay.
preferred label: SIMS

DESI dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the DESI assay.
preferred label: DESI

Auto-fluorescence dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Auto-fluorescence assay.
preferred label: Auto-fluorescence

Confocal dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Confocal assay.
preferred label: Confocal

Thick section Multiphoton MxIF dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Thick section Multiphoton MxIF assay.
preferred label: Thick section Multiphoton MxIF

Second Harmonic Generation (SHG) dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Second Harmonic Generation assay.
preferred label: Second Harmonic Generation (SHG)

Enhanced Stimulated Raman Spectroscopy (SRS) dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Enhanced Stimulated Raman Spectroscopy assay.
preferred label: Enhanced Stimulated Raman Spectroscopy (SRS)

ATACseq (bulk) dataset
type: NamedIndividual
type: Concept
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Bulk ATACseq assay.
preferred label: ATACseq (bulk)

RNAseq (bulk) dataset
type: NamedIndividual
type: Concept
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Bulk RNAseq assay.
preferred label: RNAseq (bulk)

10X Multiome dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the 10X Multiome assay.
preferred label: 10X Multiome

Molecular Cartography dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Molecular Cartography assay.
preferred label: Molecular Cartography

CosMx Transcriptomics dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the CosMx Transcriptomics assay.
preferred label: CosMx Transcriptomics

Xenium dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Xenium assay.
preferred label: Xenium

MERFISH dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the MERFISH assay.
preferred label: MERFISH

Travelling Wave Ion Mobility Spectrometry
type: NamedIndividual
type: Concept
broader: Ion mobility
definition: An ion mobility technique that utilizes a traveling wave to separate ions. In TWIMS, ions travel through a series of alternating electrical fields (traveling wave) that differentially affect the mobility of ions based on their characteristics. [Generated by an AI language model]
preferred label: TWIMS

Field Asymmetric Ion Mobility Spectrometry
type: NamedIndividual
type: Concept
broader: Ion mobility
definition: An ion mobility technique that uses a combination of high and low electric fields to separate ions. Ions are driven through a region with asymmetric electric fields, causing them to take different paths depending on their mobility characteristics. [Generated by an AI language model]
preferred label: FAIMS

Dispersive or Drift Tube Ion Mobility Spectrometry
type: NamedIndividual
type: Concept
broader: Ion mobility
definition: An ion mobility technique that employs an oscillating electric field to separate ions. Ions oscillate in a mobility cell, and their separation is based on the difference in their mobility behavior. [Generated by an AI language model]
preferred label: DTIMS

Structures for Lossless Ion Manipulations
type: NamedIndividual
type: Concept
broader: Ion mobility
definition: A technology that allows for ion manipulation without significant losses in ion intensity. SLIM devices use arrays of electrodes to guide and manipulate ions in a controlled manner. [Generated by an AI language model]
preferred label: SLIM

Cyclic Ion Mobility Spectrometry
type: NamedIndividual
type: Concept
broader: Ion mobility
definition: In cyclic ion mobility spectrometry, the ions are subjected to multiple rounds of mobility separation within the ion mobility spectrometer. This is achieved by introducing a cyclic or periodic modulation of the electric fields experienced by the ions as they traverse through the instrument. [Generated by an AI language model]
preferred label: cIMS

MS1
type: NamedIndividual
type: Concept
broader: MS scan mode

MS2
type: NamedIndividual
type: Concept
broader: MS scan mode

MS3
type: NamedIndividual
type: Concept
broader: MS scan mode

Methanol:Water (MeOH:H2O)
type: NamedIndividual
type: Concept
broader: Desorption solvent
definition: A desolvent mixture created by mixing methanol (MeOH) and water (H2O). [Generated by an AI language model]

Methanol:Ethanol (MeOH:EtOH)
type: NamedIndividual
type: Concept
broader: Desorption solvent
definition: A desolvent mixture created by mixing methanol (MeOH) and ethanol (EtOH). [Generated by an AI language model]

Acetonitrile:Water (ACN:H2O)
type: NamedIndividual
type: Concept
broader: Desorption solvent
definition: A desolvent mixture created by mixing acetonitrile (ACN) and water (H2O). [Generated by an AI language model]

Acetonitrile:Dimethylformamide (ACN:DMF)
type: NamedIndividual
type: Concept
broader: Desorption solvent
definition: A desolvent mixture created by mixing acetonitrile (ACN) and dimethylformamide (DMF). [Generated by an AI language model]

Ethanol:Water (EtOH:H2O)
type: NamedIndividual
type: Concept
broader: Desorption solvent
definition: A desolvent mixture created by mixing ethanol (EtOH) and water (H2O). [Generated by an AI language model]

Ethanol:Dimethylformamide (EtOH:DMF)
type: NamedIndividual
type: Concept
broader: Desorption solvent
definition: A desolvent mixture created by mixing ethanol (EtOH) and dimethylformamide (DMF). [Generated by an AI language model]

Robotic spotting
type: NamedIndividual
type: Concept
broader: Matrix deposition method
definition: A method of applying the matrix onto the sample surface with high precision and accuracy. It involves the use of a robotic system to dispense small droplets of the matrix solution onto the sample at predefined locations. This method is especially useful when dealing with delicate or small samples, as it allows for precise control over the location and volume of the matrix applied. By controlling the spot size and spacing, researchers can create a matrix layer that facilitates ionization while maintaining spatial resolution in IMS. [Generated by an AI language model]

Electrospray deposition
type: NamedIndividual
type: Concept
broader: Matrix deposition method
definition: A technique that uses electrospray technology to apply the matrix to the sample surface. In this method, a fine aerosol of the matrix solution is generated by electrospray and directed onto the sample. Electrospray is often used for the deposition of charged matrix droplets. These charged droplets can assist in the ionization of analytes in the sample. Electrospray deposition can offer fine control over droplet size and uniformity, which is beneficial for achieving consistent and reproducible results in IMS. [Generated by an AI language model]

Robotic spraying
type: NamedIndividual
type: Concept
broader: Matrix deposition method
definition: A method similar to robotic spotting, involves the use of a robotic system to apply the matrix solution as a fine spray or mist onto the sample surface. This method is suitable for covering larger sample areas quickly and evenly. It is particularly useful when dealing with larger sample sizes or when spatial resolution is not a primary concern. The matrix solution is atomized and sprayed onto the sample, forming a thin, uniform layer that facilitates ionization and mass spectrometric analysis. [Generated by an AI language model]

Sublimation
type: NamedIndividual
type: Concept
broader: Matrix deposition method
definition: A technique that uses a heated solid matrix compound, causing it to undergo sublimation, which transforms it directly from a solid to a gas phase. The gaseous matrix is then deposited onto the sample surface. This technique is often used when working with delicate or heat-sensitive samples, as it avoids direct contact with a liquid matrix solution. Sublimation is particularly useful for achieving fine and homogeneous matrix layers. [Generated by an AI language model]

DAN (1,5-diaminonapthalene)
type: NamedIndividual
type: Concept
broader: Preparation matrix

scATACseq dataset
type: NamedIndividual
type: Concept
broader: Dataset type (SenNet)
definition: Dataset generated from performing the scATAC-seq assay.
preferred label: scATACseq

scRNAseq dataset
type: NamedIndividual
type: Concept
broader: Dataset type (SenNet)
definition: Dataset generated from performing the scRNA-seq assay.
preferred label: scRNAseq

Perfadex Plus
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Perfusion solution
broader: Transport solution
definition: Perfadex Plus is a commercial perfusion solution used in the field of organ transplantation, particularly for preserving and transporting donor lungs. It is designed to maintain the viability and function of organs during the critical period between organ retrieval from a donor and transplantation into a recipient. [Generated by an AI language model]

10x Genomics; Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns; PN 1000283
type: NamedIndividual
type: Concept
broader: Library preparation kit
broader: Transposition reagent kit
broader: Preparation instrument kit
definition: A product bundle provided by 10x Genomics for researchers interested in performing single-cell multi-omics experiments, specifically integrating ATAC-seq and gene expression profiling. The kit is designed for 16 reactions or samples. [Generated by an AI language model]
preferred label: 10X Genomics; Chromium NextGem Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxn; PN 1000283

10x Genomics; Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxns; PN 1000285
type: NamedIndividual
type: Concept
broader: Library preparation kit
broader: Transposition reagent kit
broader: Preparation instrument kit
definition: A product bundle provided by 10x Genomics for researchers interested in performing single-cell multi-omics experiments, specifically integrating ATAC-seq and gene expression profiling. The kit is designed for 4 reactions or samples. [Generated by an AI language model]
preferred label: 10X Genomics; Chromium NextGem Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxn; PN 1000285

10x Genomics; Single Index Kit N, Set A, 96 rxns; PN 1000212
type: NamedIndividual
type: Concept
broader: Sample indexing kit
definition: A kit provided by 10x Genomics for researchers involved in sequencing projects, particularly those requiring indexing or barcoding of samples. The kit is designed for 96 reactions or samples and is labeled as "Single Index Kit N, Set A." [Generated by an AI language model]
preferred label: 10X Genomics; Single Index Kit N, Set A (96 rxn); PN 1000212

10x Genomics; Dual Index Kit TT, Set A, 96 rxns; PN 1000215
type: NamedIndividual
type: Concept
broader: Sample indexing kit
definition: A kit provided by 10x Genomics for researchers involved in sequencing projects, particularly those requiring indexing or barcoding of samples. The kit is designed for 96 reactions or samples and is labeled as "Dual Index Kit TT, Set A." [Generated by an AI language model]
preferred label: 10X Genomics; Dual Index Kit TT, Set A (96 rxn); PN 1000215

Illumina; HiSeq 3000/4000 PE Cluster Kit PE-410-1001; PN 1000283
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A cluster kit from Illumina designed for preparing samples for paired-end sequencing on the HiSeq 3000 and HiSeq 4000 sequencing systems. [Generated by an AI language model]

Illumina; NextSeq 500/550 Hi Output v2.5 Kit (150 Cycles); PN 20024907
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A kit from Illumina used for high-output sequencing on the NextSeq 500 and NextSeq 550 platforms. It is designed for 150 cycles of sequencing and is version 2.5. [Generated by an AI language model]
preferred label: Illumina; NextSeq 500/550 Hi Output Kit 150 Cycles; v2.5; PN 20024907

Illumina; NovaSeq 6000 SP Reagent v1.5 Kit (100 Cycles); PN 20028401
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A reagent kit from Illumina used with the NovaSeq 6000 sequencing system, designed for use in the S Prime (SP) flow cell format. It is version 1.5 and is designed for 100 cycles of sequencing. [Generated by an AI language model]

Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (100 Cycles); PN 20028319
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A reagent kit from Illumina used with the NovaSeq 6000 system, designed for the S1 flow cell format. It is version 1.5 and is designed for 100 cycles of sequencing. [Generated by an AI language model]

Illumina; NovaSeq 6000 S2 Reagent v1.5 Kit (100 Cycles); PN 20028316
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A reagent kit from Illumina used with the NovaSeq 6000 system, designed for the S2 flow cell format. It is version 1.5 and is designed for 100 cycles of sequencing. [Generated by an AI language model]

Illumina; NovaSeq 6000 S4 Reagent v1.5 Kit (200 Cycles); PN 20028313
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A reagent kit from Illumina used with the NovaSeq 6000 system, designed for the S4 flow cell format. It is version 1.5 and is designed for 200 cycles of sequencing. [Generated by an AI language model]

10x Genomics; Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3, 4 rxns; PN 1000092
type: NamedIndividual
type: Concept
broader: Library preparation kit
definition: A kit provided by 10x Genomics for single-cell genomics research, particularly for preparing libraries of genetic material for sequencing experiments. [Generated by an AI language model]
preferred label: 10X Genomics; Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3, 4 rxns; PN 1000092

10x Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 rxns; PN 1000184
type: NamedIndividual
type: Concept
broader: Library preparation kit
definition: A product bundle provided by 10x Genomics used to capture the spatial distribution of gene expression within tissue samples. The kit comes with 4 slides, which means researchers can analyze multiple tissue sections or samples using these slides. Additionally, it is designed for a total of 16 reactions or experiments, allowing for extensive spatial gene expression analysis. [Generated by an AI language model]
preferred label: 10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 reactions; PN 1000184

SNARE-seq2 dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the SNARE-seq2 assay.
preferred label: SNARE-seq2

10x Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 1 slides, 4 rxns; PN 1000187
type: NamedIndividual
type: Concept
broader: Library preparation kit
definition: A product bundle provided by 10x Genomics used to capture the spatial distribution of gene expression within tissue samples. The kit comes with a single slide for a total of 4 reactions or experiments, allowing for extensive spatial gene expression analysis. [Generated by an AI language model]
preferred label: 10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 1 slides, 4 reactions; PN 1000187

tissue (bulk)
type: NamedIndividual
type: Concept
broader: Assay input entity
definition: A sample that consists of a collection of cells or genetic material taken from a larger piece or mass of tissue used for conducting molecular assays. [Generated by an AI language model]

single cell
type: NamedIndividual
type: Concept
broader: Assay input entity
definition: An individual biological cell used as the starting material for a single-cell assay, where the goal is to analyze the molecular content of that specific cell. [Generated by an AI language model]

single nucleus
type: NamedIndividual
type: Concept
broader: Assay input entity
definition: A single isolated nucleus used as the starting material for a molecular assay (e.g., DNA or RNA sequencing) to analyze the genetic or epigenetic information from that nucleus. [Generated by an AI language model]

spot
type: NamedIndividual
type: Concept
broader: Assay input entity
definition: A localized region within these assays where the sample is concentrated or applied, allowing for precise analysis or processing. The size and nature of the spot can vary depending on the specific assay and its requirements. [Generated by an AI language model]

area of interest
type: NamedIndividual
type: Concept
broader: Assay input entity
definition: A specific region or subset of the sample or specimen that is the focus of the assay. It is the part of the sample that you want to analyze or study using the assay. [Generated by an AI language model]

Nucleic acid + protein
type: NamedIndividual
type: Concept
broader: Analyte class

10x Genomics; Visium Human Transcriptome Probe Kit v2 - Small; PN 1000466
type: NamedIndividual
type: Concept
broader: Oligo probe panel

nL/min
type: NamedIndividual
type: Concept
broader: Desorption solvent flow rate unit
broader: LC flow rate unit

Negative ion mode
type: NamedIndividual
type: Concept
broader: Mass analysis polarity

Positive ion mode
type: NamedIndividual
type: Concept
broader: Mass analysis polarity

Negative and positive ion mode
type: NamedIndividual
type: Concept
broader: Mass analysis polarity

MALDI-2
type: NamedIndividual
type: Concept
broader: MS ionization technique

SIMS-C60
type: NamedIndividual
type: Concept
broader: MS ionization technique

SIMS-H20
type: NamedIndividual
type: Concept
broader: MS ionization technique

10x Genomics; Dual Index Kit TS, Set A; PN 1000251
type: NamedIndividual
type: Concept
broader: Sample indexing kit
definition: A kit provided by 10x Genomics for researchers involved in sequencing projects, particularly those requiring indexing or barcoding of samples. The kit is labeled as "Dual Index Kit TS, Set A." [Generated by an AI language model]
preferred label: 10X Genomics; Dual Index Kit TS, Set A; PN 1000251

Illumina; NovaSeq X Series 10B Reagent Kit (300 Cycle); PN 20085594
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A high-capacity reagent kit from Illumina used with the NovaSeq X series system, capable of generating 10 billion paired-end sequencing reads with a read length of 300 base pairs. [Generated by an AI language model]

Illumina; NovaSeq X Series 10B Reagent Kit (200 Cycle); PN 20085595
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A high-capacity reagent kit from Illumina used with the NovaSeq X series system, capable of generating 10 billion paired-end sequencing reads with a read length of 200 base pairs. [Generated by an AI language model]

Illumina; NovaSeq X Series 10B Reagent Kit (100 Cycle); PN 20085596
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A high-capacity reagent kit from Illumina used with the NovaSeq X series system, capable of generating 10 billion paired-end sequencing reads with a read length of 100 base pairs. [Generated by an AI language model]

Illumina; NovaSeq X Series 1.5B Reagent Kit (100 Cycle); PN 20104703
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A high-capacity reagent kit from Illumina used with the NovaSeq X series system, capable of generating 1.5 billion paired-end sequencing reads with a read length of 100 base pairs. [Generated by an AI language model]

Illumina; NovaSeq X Series 1.5B Reagent Kit (200 Cycle); PN 20104704
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A high-capacity reagent kit from Illumina used with the NovaSeq X series system, capable of generating 1.5 billion paired-end sequencing reads with a read length of 200 base pairs. [Generated by an AI language model]

Illumina; NovaSeq X Series 1.5B Reagent Kit (300 Cycle); PN 20104705
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A high-capacity reagent kit from Illumina used with the NovaSeq X series system, capable of generating 1.5 billion paired-end sequencing reads with a read length of 300 base pairs. [Generated by an AI language model]

Heated electrospray ionization
type: NamedIndividual
type: Concept
broader: MS ionization technique
definition: HESI is a variant of ESI that incorporates additional heating of the nebulizing gas and the capillary emitter. The use of heat can improve the ionization efficiency for certain analytes, especially those that are less volatile or thermally labile. HESI is often employed when traditional ESI doesn't produce satisfactory ionization for specific compounds. The increased temperature helps to generate ions more effectively, making it useful for a broader range of analytes. [Generated by an AI language model]
preferred label: HESI

mL/min
type: NamedIndividual
type: Concept
broader: LC flow rate unit

Liquid Extraction Surface Analysis
type: NamedIndividual
type: Concept
broader: Spatial sampling technique
definition: LESA is an automated liquid micro-extraction technique used in combination with mass spectrometry. It involves the extraction of analytes directly from a surface (e.g., a tissue section or a sample spot on a plate) and their subsequent analysis by mass spectrometry. LESA is often used for the analysis of small molecules, lipids, and peptides. [Generated by an AI language model]
preferred label: LESA

Microscale Liquid Extraction Surface Analysis
type: NamedIndividual
type: Concept
broader: Spatial sampling technique
definition: microLESA is a technique used to extract analytes from a surface, but it operates at a smaller scale. It is well-suited for analyzing micro-sized samples, such as single cells or small tissue sections. microLESA can be used for the targeted analysis of specific regions in a sample, similar to LCM but with mass spectrometry-based detection. [Generated by an AI language model]
preferred label: microLESA

Microscale Pots for Analysis of Transferred Samples
type: NamedIndividual
type: Concept
broader: Spatial sampling technique
definition: microPOTS is another miniaturized sample preparation technique designed for LC-MS analysis. It is particularly useful for analyzing very small sample volumes, making it valuable for applications where sample quantity is limited or where high sensitivity is required. It's often used in proteomics and metabolomics research. [Generated by an AI language model]
preferred label: microPOTS

Profiling
type: NamedIndividual
type: Concept
broader: Spatial sampling type
definition: Profiling, in this context, typically involves the systematic collection of data from various regions or specific points within a sample. The goal is to analyze and compare the abundance of specific analytes, such as metabolites, lipids, peptides, or proteins, in different areas of a tissue or sample. Spatial profiling does not create a visual image but rather generates data that can be used to create spatial maps or concentration profiles. [Generated by an AI language model]

Imaging
type: NamedIndividual
type: Concept
broader: Spatial sampling type
definition: Imaging, in the context of spatial sampling in LC-MS, involves generating two-dimensional or three-dimensional visual representations of the distribution of specific analytes within a sample. It provides a direct visualization of the spatial distribution of molecules across the sample's surface. [Generated by an AI language model]

2D Imaging Mass Cytometry dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the 2D Imaging Mass Cytometry assay.
preferred label: 2D Imaging Mass Cytometry

nanoSPLITS
type: NamedIndividual
type: Concept
broader: Spatial sampling technique

nA*hr/mm2
type: NamedIndividual
type: Concept
broader: Area normalized ion dose unit
definition: The measure of the dose of ion delivery to a sample in ion beam techniques. It combines the current (nanoamperes, nA) and time (hours, hr) over a specific area (square millimeters, mm²). [Generated by an AI language model]

10x Genomics; Chromium Single Cell 3' Library & Gel Bead Kit, 4 rxns; PN 120267
type: NamedIndividual
type: Concept
broader: Library preparation kit
definition: A kit provided by 10x Genomics for single-cell genomics research, particularly for preparing libraries of genetic material for sequencing experiments. [Generated by an AI language model]
preferred label: 10X Genomics; Chromium Single Cell 3' Library & Gel Bead Kit, 4 rxns; PN 120267

GeoMx (NGS) dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the GeoMx (NGS) assay.
preferred label: GeoMx (NGS)

GeoMx (nCounter) dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the GeoMX (nCounter) assay.
preferred label: GeoMx (nCounter)

Visium (no probes) dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Visium (no probes) assay.
preferred label: Visium (no probes)

Visium (with probes) dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Visium (with probes) assay.
preferred label: Visium (with probes)

Automated segmentation
type: NamedIndividual
type: Concept
broader: ROI segmentation strategy
definition: Automated segmentation employs optimized algorithms to delineate tissue compartments based on morphology markers, enhancing the spatial transcriptomic strategy's precision in region of interest segmentation within a defined spatial biology context. [Generated by an AI language model]

Manual segmentation
type: NamedIndividual
type: Concept
broader: ROI segmentation strategy
definition: Manual segmentation, in the context of spatial transcriptomics' region of interest segmentation strategy, involves the meticulous, by-hand delineation of marker-defined areas within a specified region of interest in spatial biology. [Generated by an AI language model]

10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome, 4 rxns x 1 BC; PN 1000474
type: NamedIndividual
type: Concept
broader: Oligo probe panel

10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome 4 rxns x 4 BC; PN 1000475
type: NamedIndividual
type: Concept
broader: Oligo probe panel

ATACseq dataset
type: NamedIndividual
type: Concept
broader: Dataset type
definition: Dataset generated from performing the ATACseq assay.
preferred label: ATACseq

RNAseq dataset
type: NamedIndividual
type: Concept
broader: Dataset type
definition: Dataset generated from performing the RNAseq assay.
preferred label: RNAseq

RNAseq (with probes) dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the RNAseq (with probes) assay.
preferred label: RNAseq (with probes)

nanoSPLITS dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the nanoSPLITS assay.
preferred label: nanoSPLITS

Illumina; NovaSeq 6000 S1 Reagent Kit (200 Cycles); PN 20012864
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A reagent kit from Illumina used with the NovaSeq 6000 system, designed for the S1 flow cell format and is designed for 200 cycles of sequencing. [Generated by an AI language model]

Segmentation Mask dataset
type: NamedIndividual
type: Concept
broader: Derived dataset type
definition: Dataset generated from performing segmentation mask pipeline.
preferred label: Segmentation Mask

Phenocycler-Fusion 1.0
type: NamedIndividual
type: Concept
broader: Acquisition instrument model

Custom: Multiphoton
type: NamedIndividual
type: Concept
broader: Acquisition instrument model

Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (300 Cycles); PN 20028317
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A reagent kit from Illumina used with the NovaSeq 6000 system, designed for the S1 flow cell format. It is version 1.5 and is designed for 300 cycles of sequencing. [Generated by an AI language model]

Illumina; NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles); PN 20028312
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A reagent kit from Illumina used with the NovaSeq 6000 system, designed for the S4 flow cell format. It is version 1.5 and is designed for 300 cycles of sequencing. [Generated by an AI language model]

10x Genomics; Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome, 1 slides, 4 rxns; PN 1000338
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome, 1 slides, 4 reactions; PN 1000338

10x Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Human Transcriptome, 6.5mm, 4 rxns; PN 1000520
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Human Transcriptome, 6.5mm, 4 reactions; PN 1000520

10x Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Human Transcriptome, 11 mm, 2 rxns; PN 1000522
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Human Transcriptome, 11 mm, 2 reactions; PN 1000522

Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (100 Cycles); PN 20046811
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit

10x Genomics; Visium FFPE Reagent Kit v2-Small; PN 1000436
type: NamedIndividual
type: Concept
broader: Preparation instrument kit
preferred label: 10X Genomics; Visium FFPE Reagent Kit v2-Small, PN 1000436

10x Genomics; Chromium Next GEM Chip Q Single Cell Kit, 16 rxns; PN 1000422
type: NamedIndividual
type: Concept
broader: Preparation instrument kit
preferred label: 10X Genomics; Chromium Next GEM Chip Q Single Cell Kit, 16 rxns; PN 1000422

10x Genomics; Visium Human Transcriptome Probe Kit-Small; PN 1000363
type: NamedIndividual
type: Concept
broader: Oligo probe panel

DNA + RNA
type: NamedIndividual
type: Concept
broader: Analyte class

MUSIC
type: NamedIndividual
type: Concept
broader: Dataset type
definition: Dataset generated from performing the MUSIC assay.

Hematoxylin and 3,3′-Diaminobenzidine stain
type: NamedIndividual
type: Concept
broader: Stain name
definition: Hematoxylin and 3,3′-Diaminobenzidine (H-DAB) staining is a technique used in immunohistochemistry to visualize specific antigens within tissues. Hematoxylin stains cell nuclei blue, while DAB produces a brown precipitate at antibody-binding sites, highlighting the presence and location of target proteins. [Generated by an AI language model]
preferred label: H-DAB

Biops buffer
type: NamedIndividual
type: Concept
broader: Preparation medium

Trumps fixative
type: NamedIndividual
type: Concept
broader: Preparation medium

2% PFA/2.5% Glutaraldehyde
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium

Cryo-EM
type: NamedIndividual
type: Concept
broader: Storage medium

10x Genomics; Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, 16 rxns; PN 1000121
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, 16 rxns; PN 1000121

10x Genomics; Chromium Next GEM Single Cell 3' HT Kit v3.1, 48 rxns; PN 1000348
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Chromium Next GEM Single Cell 3' HT Kit v3.1, 48 rxns; PN 1000348

10x Genomics; Chromium Next GEM Single Cell 3' HT Kit v3.1, 8 rxns; PN 1000370
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Chromium Next GEM Single Cell 3' HT Kit v3.1, 8 rxns; PN 1000370

10x Genomics; Chromium Next GEM Single Cell 3' Kit v3.1, 16 rxns; PN 1000268
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Chromium Next GEM Single Cell 3' Kit v3.1, 16 rxns; PN 1000268

10x Genomics; Chromium Next GEM Single Cell 3' Kit v3.1, 4 rxns; PN 1000269
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Chromium Next GEM Single Cell 3' Kit v3.1, 4 rxns; PN 1000269

10x Genomics; Chromium Next GEM Single Cell 5' Kit v2, 16 rxns; PN 1000263
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Chromium Next GEM Single Cell 5' Kit v2, 16 rxns; PN 1000263

10x Genomics; Chromium Next GEM Single Cell 5' Kit v2, 4 rxns; PN 1000265
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Chromium Next GEM Single Cell 5' Kit v2, 4 rxns; PN 1000265

Parse Biosciences; Evercode WT v2 Kit, 48 rxns; PN ECW02030
type: NamedIndividual
type: Concept
broader: Library preparation kit

Parse Biosciences; Evercode WT Mini v2 Kit, 12 rxns; PN ECW02010
type: NamedIndividual
type: Concept
broader: Library preparation kit

Illumina; TruSeq Stranded mRNA Library Prep (48 samples); PN 20020594
type: NamedIndividual
type: Concept
broader: Library preparation kit

Illumina; TruSeq Stranded mRNA Library Prep (96 samples); PN 20020595
type: NamedIndividual
type: Concept
broader: Library preparation kit

Parse Biosciences; Fragmentation Reagents; PN WX100
type: NamedIndividual
type: Concept
broader: Sample indexing kit

Parse Biosciences; UDI Plate - WT; PN UDI1001
type: NamedIndividual
type: Concept
broader: Sample indexing kit

Illumina; TruSeq RNA Single Indexes Set A (12 Indexes, 48 Samples); PN 20020492
type: NamedIndividual
type: Concept
broader: Sample indexing kit

Illumina; TruSeq RNA Single Indexes Set B (12 Indexes, 48 Samples); PN 20020493
type: NamedIndividual
type: Concept
broader: Sample indexing kit

Illumina; TruSeq RNA CD Index Plate (96 Indexes, 96 Samples); PN 20019792
type: NamedIndividual
type: Concept
broader: Sample indexing kit

Illumina; IDT for Illumina - TruSeq RNA UD Indexes v2 (96 Indexes, 96 Samples); PN 20040871
type: NamedIndividual
type: Concept
broader: Sample indexing kit

Integrated DNA Technologies: Custom DNA Oligos
type: NamedIndividual
type: Concept
broader: Sample indexing kit

Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (200 Cycles); PN 20046812
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit

Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (300 Cycles); PN 20046813
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit

Illumina; NextSeq 2000 P3 Reagent Kit (300 Cycles); PN 20040561
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit

10x Genomics; Visium Spatial for FFPE Gene Expression Kit, Mouse Transcriptome, 4 rxns; PN 1000339
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Visium Spatial for FFPE Gene Expression Kit, Mouse Transcriptome, 4 rxns; PN 1000339

NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-AB
type: NamedIndividual
type: Concept
broader: Sample indexing kit
definition: NGS readout reagents for GeoMx DSP RNA and protein analysis. Includes two Seq Code primer plates (A&B) and two universal enzyme master mixes.

NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-CD
type: NamedIndividual
type: Concept
broader: Sample indexing kit
definition: NGS readout reagents for GeoMx DSP RNA and protein analysis. Includes two Seq Code primer plates (C&D) and two universal enzyme master mixes.

NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-EF
type: NamedIndividual
type: Concept
broader: Sample indexing kit
definition: NGS readout reagents for GeoMx DSP RNA and protein analysis. Includes two Seq Code primer plates (E&F) and two universal enzyme master mixes.

NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-GH
type: NamedIndividual
type: Concept
broader: Sample indexing kit
definition: NGS readout reagents for GeoMx DSP RNA and protein analysis. Includes two Seq Code primer plates (G&H) and two universal enzyme master mixes.

Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (200 Cycles); PN 20028318
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit

Illumina; NextSeq 2000 P3 Reagents Kit (100 Cycles); PN 20040559
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit

10x Genomics; Visium Mouse Transcriptome Probe Kit - Small; PN 1000365
type: NamedIndividual
type: Concept
broader: Oligo probe panel

NanoString Technologies; GeoMx Human Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-HuWTA-4
type: NamedIndividual
type: Concept
broader: Oligo probe panel
definition: RNA Probe set that targets 18,000+ transcripts for human protein coding genes plus ERCC negative controls to profile the whole transcriptome. Excludes uninformative high expressing targets such as ribosomal subunits. Includes RNA probes designed for Illumina NGS readout with the Seq Code library prep.

NanoString Technologies; GeoMx Mouse Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-MsWTA-4
type: NamedIndividual
type: Concept
broader: Oligo probe panel
definition: RNA Probe set that targets 21,000+ transcripts for mouse protein coding genes plus ERCC negative controls to profile the whole transcriptome. Excludes uninformative high expressing targets such as ribosomal subunits. Includes RNA probes designed for Illumina NGS readout with the Seq Code library prep.

10x Genomics; Chromium Next GEM Automated Single Cell 5' Kit v2, 24 rxns; PN 1000290
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Chromium Next GEM Automated Single Cell 5' Kit v2, 24 rxns; PN 1000290

10x Genomics; Chromium Next GEM Automated Single Cell 5' Kit v2, 4 rxns; PN 1000298
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Chromium Next GEM Automated Single Cell 5' Kit v2, 4 rxns; PN 1000298

10x Genomics; Chromium Next GEM Chip K Single Cell Kit, 48 rxns; PN 1000286
type: NamedIndividual
type: Concept
broader: Preparation instrument kit
preferred label: 10X Genomics; Chromium Next GEM Chip K Single Cell Kit, 48 rxns; PN 1000286

10x Genomics; Chromium Next GEM Chip K Single Cell Kit, 16 rxns; PN 1000287
type: NamedIndividual
type: Concept
broader: Preparation instrument kit
preferred label: 10X Genomics; Chromium Next GEM Chip K Single Cell Kit, 16 rxns; PN 1000287

Illumina; NextSeq 500/550 Mid Output v2.5 Kit (150 Cycles); PN 20024904
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A kit from Illumina used for mid-output sequencing on the NextSeq 500 and NextSeq 550 platforms. It is designed for 150 cycles of sequencing and is version 2.5. [Generated by an AI language model]
preferred label: Illumina; NextSeq 500/550 Mid Output Kit 150 Cycles v2.5; PN 20024904

Modified Davidson's Fixative
type: NamedIndividual
type: Concept
broader: Preparation medium

Alpha-MEM
type: NamedIndividual
type: Concept
broader: Preparation medium

Growth media
type: NamedIndividual
type: Concept
broader: Preparation medium

10x Genomics; Chromium Next GEM Chip K Automated Single Cell Kit, 48 rxns; PN 1000289
type: NamedIndividual
type: Concept
broader: Preparation instrument kit
preferred label: 10X Genomics; Chromium Next GEM Chip K Automated Single Cell Kit, 48 rxns; PN 1000289

10x Genomics; Automated Library Construction Kit, 24 rxns; PN 1000428
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Automated Library Construction Kit, 24 rxns; PN 1000428

10x Genomics; Chromium Next GEM Single Cell Fixed RNA Hybridization & Library Kit, 4 rxns; PN 1000415
type: NamedIndividual
type: Concept
broader: Library preparation kit
preferred label: 10X Genomics; Chromium Next GEM Single Cell Fixed RNA Hybridization & Library Kit, 4 rxns; PN 1000415

10x Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 64 rxns; PN 1000456
type: NamedIndividual
type: Concept
broader: Oligo probe panel
preferred label: 10X Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 64 rxns; PN 1000456

New England BioLabs; NEBNext Ultra II RNA Library Prep Kit for Illumina; PN E7770
type: NamedIndividual
type: Concept
broader: Library preparation kit

10x Genomics; Chromium Next GEM Chip G Single Cell Kit, 48 rxns; PN 1000120
type: NamedIndividual
type: Concept
broader: Preparation instrument kit
preferred label: 10X Genomics; Chromium Next GEM Chip G Single Cell Kit, 48 rxns; PN 1000120

10x Genomics; Chromium Next GEM Chip G Single Cell Kit, 16 rxns; PN 1000127
type: NamedIndividual
type: Concept
broader: Preparation instrument kit
preferred label: 10X Genomics; Chromium Next GEM Chip G Single Cell Kit, 16 rxns; PN 1000127

10x Genomics; Chromium i7 Sample Index Plate, 96 rxns; PN 220103
type: NamedIndividual
type: Concept
broader: Sample indexing kit
preferred label: 10X Genomics; Chromium i7 Sample Index Plate (96 rxn); PN 220103

Illumina; NextSeq 500/550 Hi Output v2.5 Kit (75 Cycles); PN 20024906
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
preferred label: Illumina; NextSeq 500/550 Hi Output Kit 75 Cycles v2.5; PN 20024906

10x Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 16 rxns; PN 1000420
type: NamedIndividual
type: Concept
broader: Oligo probe panel
preferred label: 10X Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 16 rxns; PN 1000420

10x Genomics; Visium Human Transcriptome Probe Kit-Large; PN 1000364
type: NamedIndividual
type: Concept
broader: Oligo probe panel

Resolve
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Resolve assay.

Stereo-seq
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Stereo-seq assay.

Hydroxypropyl Methylcellulose-Polyvinylpyrrolidone
type: NamedIndividual
type: Concept
broader: Preparation medium
broader: Storage medium
definition: A medium that combines Hydroxypropyl Methylcellulose (HPMC) and Polyvinylpyrrolidone (PVP), often used in biological and biomedical applications to stabilize samples, control viscosity, and protect cellular structures during processing and analysis. [Generated by an AI language model]
preferred label: HPMC-PVP

Stored in desiccator
type: NamedIndividual
type: Concept
broader: Storage method
definition: Keeping sample specimens in a sealed container with a desiccant to maintain a low-humidity environment and protect them from moisture damage. [Generated by an AI language model]

Saturated lipid
type: NamedIndividual
type: Concept
broader: Analyte class

Unsaturated lipid
type: NamedIndividual
type: Concept
broader: Analyte class

Seq-Scope dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Seq-Scope assay.
preferred label: Seq-Scope

Concentrated quench buffer
type: NamedIndividual
type: Concept
broader: Storage medium
definition: A concentrated quench buffer is a solution used to rapidly stop a chemical or enzymatic reaction by neutralizing reactants or inhibiting enzymes, often containing agents like acids, bases, or inhibitors. [Generated by an AI language model]

Illumina; NovaSeq X Series 25B Reagent Kit (300 Cycle); PN 20104706
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A high-capacity reagent kit from Illumina used with the NovaSeq X series system, includes a 25B flow cell with eight lanes and the necessary reagents to support a single 300-cycle sequencing run. [Generated by an AI language model]

10x Genomics; Chromium Next GEM Single Cell Fixed RNA Mouse Transcriptome Probe Kit, 64 rxns; PN 1000492
type: NamedIndividual
type: Concept
broader: Oligo probe panel

10x Genomics; Chromium GEM-X Single Cell 5' Kit v3, 16 rxns; PN 1000699
type: NamedIndividual
type: Concept
broader: Library preparation kit

10x Genomics; Xenium Human Multi-Tissue and Cancer Panel v1; PN 1000626
type: NamedIndividual
type: Concept
broader: Oligo probe panel

DART-FISH
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the DART-FISH assay.

seqFISH
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the seqFISH assay.

10x Genomics; Library Construction Kit C, 4 rxns; PN 1000689
type: NamedIndividual
type: Concept
broader: Library preparation kit

10x Genomics; Library Construction Kit C, 16 rxns; PN 1000694
type: NamedIndividual
type: Concept
broader: Library preparation kit

10x Genomics; Chromium GEM-X Single Cell 3' Kit v4, 16 rxns; PN 1000691
type: NamedIndividual
type: Concept
broader: Preparation instrument kit

Lipid + metabolite
type: NamedIndividual
type: Concept
broader: Analyte class

Object x Analyte dataset
type: NamedIndividual
type: Concept
broader: Derived dataset type
preferred label: Object x Analyte

MERSCOPE
type: NamedIndividual
type: Concept
broader: Acquisition instrument model

MS Lipidomics
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the MS Lipidomics assay.

Element Biosciences; AVITI 2x75 Sequencing Kit Cloudbreak FS High Output (184 Cycles); PN 860-00015
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit

CyTOF
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the CyTOF assay.

Standard BioTools; Maxpar Phosphoprotein Staining Kit; PN 201604
type: NamedIndividual
type: Concept
broader: Antibody reagent kit

Standard BioTools; Maxpar Nuclear Antigen Staining Kit; PN 201603
type: NamedIndividual
type: Concept
broader: Antibody reagent kit

Standard BioTools; Maxpar Cytoplasmic/Secreted Antigen Staining Kit; PN 201602
type: NamedIndividual
type: Concept
broader: Antibody reagent kit

Standard BioTools; Maxpar Cell Surface Staining Kit; PN 201601
type: NamedIndividual
type: Concept
broader: Antibody reagent kit

Standard BioTools; Cell-ID Cisplatin 100 uL; PN 201064
type: NamedIndividual
type: Concept
broader: Viability reagent kit

Standard BioTools; Cell-ID Cisplatin-194Pt 100 uL; PN 201194
type: NamedIndividual
type: Concept
broader: Viability reagent kit

Standard BioTools; Cell-ID Cisplatin-195Pt 100 uL; PN 201195
type: NamedIndividual
type: Concept
broader: Viability reagent kit

Standard BioTools; Cell-ID Cisplatin-196Pt 100 uL; PN 201196
type: NamedIndividual
type: Concept
broader: Viability reagent kit

Standard BioTools; Cell-ID Cisplatin-198Pt 100 uL; PN 201198
type: NamedIndividual
type: Concept
broader: Viability reagent kit

Standard BioTools; Cell-ID Intercalator-103Rh 500 um; PN 201103A
type: NamedIndividual
type: Concept
broader: Viability reagent kit

Standard BioTools; Cell-ID Intercalator-103Rh 2,000 um; PN 201103B
type: NamedIndividual
type: Concept
broader: Viability reagent kit

Sigma Aldrich; Cisplatin 25mg; PN P4394
type: NamedIndividual
type: Concept
broader: Viability reagent kit

Standard BioTools; CyTOF Calibration Beads; PN 201073
type: NamedIndividual
type: Concept
broader: Instrument calibration bead kit

Standard BioTools; EQ Four Element Calibration Beads 100 mL; PN 201078
type: NamedIndividual
type: Concept
broader: Instrument calibration bead kit

Standard BioTools; EQ Six Element Calibration Beads 100 mL; PN 201245
type: NamedIndividual
type: Concept
broader: Instrument calibration bead kit

cells/mL
type: NamedIndividual
type: Concept
broader: Loaded cell concentration unit

Nucleus + cell
type: NamedIndividual
type: Concept
broader: Suspension entity type

1X fixation & permeabilization buffer
type: NamedIndividual
type: Concept
broader: Preparation medium

10x Genomics; Xenium Prime 5K Human Pan Tissue & Pathways Panel; PN 1000724
type: NamedIndividual
type: Concept
broader: Oligo probe panel

1X quench buffer
type: NamedIndividual
type: Concept
broader: Storage medium

DBiT-seq dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the DBiT-seq assay.
preferred label: DBiT-seq

Singular Genomics G4X dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Singular Genomics G4X assay.
preferred label: Singular Genomics G4X

NanoString Technologies; CosMx Human Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-H-USCP-1KP-R
type: NamedIndividual
type: Concept
broader: Oligo probe panel
definition: The CosMx™ Human Universal Cell Characterization Panel includes 1000 targets covering cell types, cell states, and cell signaling across a variety of tissue types. Ten negative control targets are also included for analysis of results. The panel is configured as a 950-target core plus controls and includes a 50-target add-on that could be replaced with a custom add-on with targets of your choosing. The core 960 targets (950 genes and 10 controls) in the panel are covered by the CosMx Hs UCC RNA Probe Mix. The CosMx Hs UCC RNA Add-On (50) Probe Mix covers an additional 50 genes and can alternatively be replaced with a CosMx Custom Add-On panel of between 7-50 genes. Volume is for 4 slides and can be run in either a 2X2 or 1X4 Slide Run configuration.

10x Genomics; Visium Mouse Transcriptome Probe Kit v2.0 - Small; PN 1000667
type: NamedIndividual
type: Concept
broader: Oligo probe panel

10x Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Mouse Transcriptome, 6.5mm, 4 rxns; PN 1000521
type: NamedIndividual
type: Concept
broader: Library preparation kit

MALDI timsTOF Flex Prototype
type: NamedIndividual
type: Concept
broader: Acquisition instrument model
definition: A prototype of MALDI timsTOF FleX

CosMx Proteomics dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the CosMx Proteomics assay.
preferred label: CosMx Proteomics

NanoString Technologies; CosMx Human Immuno-Oncology Panel (Protein, 64 Plex); PN CMX-H-IOP-64P-P
type: NamedIndividual
type: Concept
broader: Oligo probe panel

NanoString Technologies; CosMx Mouse Neuroscience Panel (Protein, 64 Plex); PN CMX-M-Neuro-64P-P
type: NamedIndividual
type: Concept
broader: Oligo probe panel

picogram per microliter
type: NamedIndividual
type: Concept
broader: Library concentration unit
definition: A mass unit density which is equal to mass of an object in picograms divided by the volume in microliters.
preferred label: pg/ul

10x Genomics; Library Construction Kit, 16 rxns; PN 1000190
type: NamedIndividual
type: Concept
broader: Library preparation kit

FACS dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Fluorescence-Activated Cell Sorting (FACS) assay.
preferred label: FACS

Olink dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Olink assay.
preferred label: Olink

10x Genomics; Xenium Mouse Multi-Tissue Atlassing Panel; PN 1000627
type: NamedIndividual
type: Concept
broader: Oligo probe panel

10x Genomics; Xenium Human Lung Gene Expression Panel; PN 1000601
type: NamedIndividual
type: Concept
broader: Oligo probe panel

10x Genomics; Xenium Custom Gene Expression Panel, (51-100 genes); PN 1000561
type: NamedIndividual
type: Concept
broader: Oligo probe panel
preferred label: 10x Genomics; Xenium Custom Gene Expression Panel (51-100 genes); PN 1000561

10x Genomics; Xenium Custom Gene Expression Panel (up to 50 genes); PN 1000464
type: NamedIndividual
type: Concept
broader: Oligo probe panel

10x Genomics; Xenium Human Colon Gene Expression Panel; PN 1000642
type: NamedIndividual
type: Concept
broader: Oligo probe panel

4i dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the 4i assay.
preferred label: 4i

MPLEx dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the MPLEx assay.
preferred label: MPLEx

Pixel-seqV2 dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Pixel-seqV2 assay.
preferred label: Pixel-seqV2

Visium HD dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the Visium HD assay.
preferred label: Visium HD

NanoString Technologies; CosMx Mouse Neuroscience Panel (RNA, 1000 Plex); PN CMX-M-NEUP-R
type: NamedIndividual
type: Concept
broader: Oligo probe panel

NanoString Technologies; CosMx Hs WTX RNA Panel Kit, 2 slides: PN 121500047
type: NamedIndividual
type: Concept
broader: Oligo probe panel

NanoString Technologies; CosMx Hs Univ Cell (RNA, 1000 Plex); PN 121500002
type: NamedIndividual
type: Concept
broader: Oligo probe panel

NanoString Technologies; CosMx Human 6K Discovery Panel (RNA, 6175 Plex); PN 121500041
type: NamedIndividual
type: Concept
broader: Oligo probe panel

Nano electrospray ionization
type: NamedIndividual
type: Concept
broader: MS ionization technique
definition: Nano-electrospray ionization (nESI) is a variant of electrospray ionization used in mass spectrometry that operates at extremely low flow rates (typically nanoliters per minute) through very fine emitter tips. By producing much smaller charged droplets, nESI enhances ionization efficiency, reduces sample consumption, and improves sensitivity, making it especially useful for analyzing scarce samples, biomolecules, and noncovalent complexes while preserving their native structures. [Generated by an AI language model]
preferred label: nESI

NanoString Technologies; CosMx Mouse Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-M-USCP-1KP-R
type: NamedIndividual
type: Concept
broader: Oligo probe panel

COMET dataset
type: NamedIndividual
type: Concept
broader: Dataset type
broader: Dataset type (SenNet)
definition: Dataset generated from performing the COMET assay.
preferred label: COMET

Illumina; NovaSeq 6000 SP Reagent v1.5 Kit (300 Cycles); PN 20028400
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A reagent kit from Illumina used with the NovaSeq 6000 sequencing system, designed for use in the S Prime (SP) flow cell format. It is version 1.5 and is designed for 300 cycles of sequencing. [Generated by an AI language model]

10x Genomics; Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, 16 rxns; PN 1000075
type: NamedIndividual
type: Concept
broader: Library preparation kit

10x Genomics; Chromium i7 Multiplex Kit, 96 rxns; PN 120262
type: NamedIndividual
type: Concept
broader: Sample indexing kit

10x Genomics; Chromium Single Cell B Chip Kit, 16 rxns; PN 1000074
type: NamedIndividual
type: Concept
broader: Preparation instrument kit

Illumina; NovaSeq X Series 25B Reagent Kit (100 Cycle); PN 20125967
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A high-capacity reagent kit from Illumina used with the NovaSeq X series system, includes a 25B flow cell with eight lanes and the necessary reagents to support a single 100-cycle sequencing run. [Generated by an AI language model]

Illumina; NovaSeq X Series 25B Reagent Kit (200 Cycle); PN 20125968
type: NamedIndividual
type: Concept
broader: Sequencing reagent kit
definition: A high-capacity reagent kit from Illumina used with the NovaSeq X series system, includes a 25B flow cell with eight lanes and the necessary reagents to support a single 200-cycle sequencing run. [Generated by an AI language model]

Stored on wet ice
type: NamedIndividual
type: Concept
broader: Preparation condition

10x Genomics; Chromium Next GEM Single Cell 5' HT Kit v2, 8 rxns; PN 1000374
type: NamedIndividual
type: Concept
broader: Library preparation kit

10x Genomics; Chromium Next GEM Single Cell 5' HT Kit v2, 48 rxns; PN 1000356
type: NamedIndividual
type: Concept
broader: Library preparation kit

10x Genomics; Chromium i7 Multiplex Kit N, Set A, 96 rxn; PN 1000084
type: NamedIndividual
type: Concept
broader: Sample indexing kit

10x Genomics; Chromium Single Cell ATAC Library & Gel Bead Kit, 16 rxns; PN 1000110
type: NamedIndividual
type: Concept
broader: Library preparation kit
broader: Transposition reagent kit

10x Genomics; Chromium Chip E Single Cell ATAC Kit, 48 rxns; PN 1000155
type: NamedIndividual
type: Concept
broader: Preparation instrument kit

10x Genomics; Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, 16 rxns; PN 1000175
type: NamedIndividual
type: Concept
broader: Library preparation kit
broader: Transposition reagent kit

Illumina; Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit; PN 20034197
type: NamedIndividual
type: Concept
broader: Transposition reagent kit

Virtual Histology dataset
type: NamedIndividual
type: Concept
broader: Dataset type
definition: Dataset generated from performing the Virtual Histology assay.
preferred label: Virtual Histology

RNA + protein
type: NamedIndividual
type: Concept
broader: Analyte class

Raman Imaging dataset
type: NamedIndividual
type: Concept
broader: Dataset type
definition: Dataset generated from performing the Raman Imaging assay.
preferred label: Raman Imaging

STARmap dataset
type: NamedIndividual
type: Concept
broader: Dataset type
definition: Dataset generated from performing the STARmap assay.
preferred label: STARmap

10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome 16 rxns x 16 BC; PN 1000547
type: NamedIndividual
type: Concept
broader: Oligo probe panel

Lipid + metabolite + protein
type: NamedIndividual
type: Concept
broader: Analyte class

iCLAP dataset
type: NamedIndividual
type: Concept
broader: Dataset type
definition: Dataset generated from performing the iCLAP assay.
preferred label: iCLAP

MACSima dataset
type: NamedIndividual
type: Concept
broader: Dataset type
definition: Dataset generated from performing the MACSima assay.
preferred label: MACSima

10x Genomics; GEM-X Flex Human Transcriptome Probe Kit, 16 samples; PN 1000785
type: NamedIndividual
type: Concept
broader: Oligo probe panel

Nuclease-free water
type: NamedIndividual
type: Concept
broader: Storage medium
definition: Ultra-pure water that has been treated and validated to be free of detectable nuclease activity, including RNases and DNases, and is intended for use in molecular biology applications to prevent degradation of nucleic acids. [Generated by an AI language model]

MAPCA (methyl 3-(4-aminophenyl)-2-cyanoacrylate)
type: NamedIndividual
type: Concept
broader: Preparation matrix

10x Genomics; Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit, 16 rxns; PN 1000414
type: NamedIndividual
type: Concept
broader: Library preparation kit

Square binning
type: NamedIndividual
type: Concept
broader: Spatial discretization method

Hexagonal binning
type: NamedIndividual
type: Concept
broader: Spatial discretization method

Illumina Spatial ver0 dataset
type: NamedIndividual
type: Concept
broader: Dataset type
definition: Dataset generated from performing the Illumina Spatial ver0 assay.
preferred label: Illumina Spatial ver0

NanoString Technologies; GeoMx Human IO Proteome Atlas, 4 slides; PN 121300160
type: NamedIndividual
type: Concept
broader: Oligo probe panel
definition: The NanoString Technologies GeoMx Human IO Proteome Atlas Kit provides a 570+ plex protein profiling panel designed for spatial proteomics on Formalin-Fixed, Paraffin-Embedded (FFPE) tissues. This kit covers 4 slides per aliquot, focusing on immune, immuno-oncology, and metabolism targets.

Fluorophores
type: NamedIndividual
type: Concept
broader: Stain name
definition: A chemical compound that can re-emit light upon light excitation. [Generated by an AI language model]

DNA Methylation dataset
type: NamedIndividual
type: Concept
broader: Dataset type
definition: Dataset generated from performing the DNA Methylation assay.
preferred label: DNA Methylation

10x Genomics; Xenium Human Skin Gene Expression Panel; PN 1000643
type: NamedIndividual
type: Concept
broader: Oligo probe panel

Source storage duration unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'source storage duration unit' field within the context of the HuBMAP project.
narrower: minute
narrower: hour
narrower: day
narrower: month
narrower: year

Preparation medium
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'preparation medium' field within the context of the HuBMAP project.
narrower: NP40 Lysis Buffer
narrower: Unknown
narrower: PAXgene tissue system
narrower: Dulbecco's Modified Eagle Medium
narrower: None
narrower: RNALater
narrower: Periodate-lysine-paraformaldehyde
narrower: Ethanol
narrower: Methanol
narrower: Paraformaldehyde polymer
narrower: Neutral buffered formalin
narrower: Phosphate buffered saline solution
narrower: MACS tissue storage solution
narrower: Inflated (Agarose)
narrower: Fixed frozen OCT (Formalin, sucrose protected)
narrower: Allprotect tissue reagent (ALL)
narrower: Inflated (OCT)
narrower: Fresh frozen OCT
narrower: Fresh frozen CMC
narrower: CLARITY hydrogel
narrower: Bouin's
narrower: Fixed frozen OCT (PFA, sucrose protected)
narrower: Fixed frozen OCT (Cytofix/Cytoperm)
narrower: University of Wisconsin Solution
narrower: Histidine-Tryptophan-Ketoglutarate Solution
narrower: Fresh frozen gelatin
narrower: Perfadex Plus
narrower: Biops buffer
narrower: Trumps fixative
narrower: 2% PFA/2.5% Glutaraldehyde
narrower: Modified Davidson's Fixative
narrower: Alpha-MEM
narrower: Growth media
narrower: Hydroxypropyl Methylcellulose-Polyvinylpyrrolidone
narrower: 1X fixation & permeabilization buffer

Preparation condition
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'preparation condition' field within the context of the HuBMAP project.
narrower: Unknown
narrower: Liquid nitrogen storage
narrower: Liquid nitrogen vapor storage
narrower: Frozen on dry ice
narrower: Specimen at room temperature
narrower: Stored in refrigerator
narrower: Frozen at -20 degrees celsius
narrower: Frozen on ice
narrower: Incubated at 37 degrees celsius
narrower: Stored on wet ice

Processing time unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'processing time unit' field within the context of the HuBMAP project.
narrower: minute
narrower: hour
narrower: day

Storage medium
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'storage medium' field within the context of the HuBMAP project.
narrower: Formalin-fixed paraffin-embedded
narrower: Unknown
narrower: PAXgene tissue system
narrower: None
narrower: RNALater
narrower: Optimal cutting temperature compound
narrower: Water
narrower: Gelatin
narrower: Carboxymethylcellulose
narrower: Formic acid
narrower: Ethanol
narrower: Methanol
narrower: Paraformaldehyde polymer
narrower: Neutral buffered formalin
narrower: Phosphate buffered saline solution
narrower: MACS tissue storage solution
narrower: DMSO (no serum)
narrower: Allprotect tissue reagent (ALL)
narrower: DMSO (serum)
narrower: Tris-EDTA
narrower: 2% PFA/2.5% Glutaraldehyde
narrower: Cryo-EM
narrower: Hydroxypropyl Methylcellulose-Polyvinylpyrrolidone
narrower: Concentrated quench buffer
narrower: 1X quench buffer
narrower: Nuclease-free water

Storage method
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'storage method' field within the context of the HuBMAP project.
narrower: Unknown
narrower: Liquid nitrogen storage
narrower: Liquid nitrogen vapor storage
narrower: Frozen on dry ice
narrower: None
narrower: Specimen at room temperature
narrower: Stored in refrigerator
narrower: Frozen at -20 degrees celsius
narrower: Frozen at -80 degrees celsius
narrower: Frozen on ice
narrower: Incubated at 37 degrees celsius
narrower: Stored in desiccator

Thickness unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'thickness unit' field within the context of the HuBMAP project.
narrower: centimeter
narrower: millimeter
narrower: micrometer

Area unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'area unit' field within the context of the HuBMAP project.
narrower: square millimeter
narrower: square micrometer

Volume unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'volume unit' field within the context of the HuBMAP project.
narrower: cubic centimeter
narrower: milliliter
narrower: um^3
narrower: mm^3

Tissue weight unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'tissue weight unit' field within the context of the HuBMAP project.
narrower: kilogram
narrower: gram
narrower: milligram
narrower: microgram

Pathology distance unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'pathology distance unit' field within the context of the HuBMAP project.
narrower: centimeter
narrower: millimeter

Suspension entity type
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'suspension entity type' field within the context of the HuBMAP project.
narrower: Cell
narrower: Nucleus
narrower: cDNA
narrower: Nucleus + cell

Dataset type
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'dataset type' field within the context of the HuBMAP project.
narrower: Cell DIVE dataset
narrower: CODEX dataset
narrower: Light Sheet dataset
narrower: MIBI dataset
narrower: LC-MS dataset
narrower: HiFi-Slide dataset
narrower: Histology dataset
narrower: PhenoCycler dataset
narrower: CyCIF dataset
narrower: MALDI dataset
narrower: SIMS dataset
narrower: DESI dataset
narrower: Auto-fluorescence dataset
narrower: Confocal dataset
narrower: Thick section Multiphoton MxIF dataset
narrower: Second Harmonic Generation (SHG) dataset
narrower: Enhanced Stimulated Raman Spectroscopy (SRS) dataset
narrower: 10X Multiome dataset
narrower: Molecular Cartography dataset
narrower: CosMx Transcriptomics dataset
narrower: Xenium dataset
narrower: MERFISH dataset
narrower: SNARE-seq2 dataset
narrower: 2D Imaging Mass Cytometry dataset
narrower: GeoMx (NGS) dataset
narrower: GeoMx (nCounter) dataset
narrower: Visium (no probes) dataset
narrower: Visium (with probes) dataset
narrower: ATACseq dataset
narrower: RNAseq dataset
narrower: RNAseq (with probes) dataset
narrower: nanoSPLITS dataset
narrower: MUSIC
narrower: Resolve
narrower: Stereo-seq
narrower: Seq-Scope dataset
narrower: DART-FISH
narrower: seqFISH
narrower: MS Lipidomics
narrower: CyTOF
narrower: DBiT-seq dataset
narrower: Singular Genomics G4X dataset
narrower: CosMx Proteomics dataset
narrower: FACS dataset
narrower: Olink dataset
narrower: 4i dataset
narrower: MPLEx dataset
narrower: Pixel-seqV2 dataset
narrower: Visium HD dataset
narrower: COMET dataset
narrower: Virtual Histology dataset
narrower: Raman Imaging dataset
narrower: STARmap dataset
narrower: iCLAP dataset
narrower: MACSima dataset
narrower: Illumina Spatial ver0 dataset
narrower: DNA Methylation dataset

Dataset type (SenNet)
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'dataset type v1' field within the context of the HuBMAP project. At the moment, the SenNet consortium is using this value set.
narrower: Cell DIVE dataset
narrower: CODEX dataset
narrower: Light Sheet dataset
narrower: MIBI dataset
narrower: snATACseq dataset
narrower: snRNAseq dataset
narrower: Visium dataset
narrower: LC-MS dataset
narrower: HiFi-Slide dataset
narrower: Histology dataset
narrower: PhenoCycler dataset
narrower: CyCIF dataset
narrower: MALDI dataset
narrower: SIMS dataset
narrower: DESI dataset
narrower: Auto-fluorescence dataset
narrower: Confocal dataset
narrower: Thick section Multiphoton MxIF dataset
narrower: Second Harmonic Generation (SHG) dataset
narrower: Enhanced Stimulated Raman Spectroscopy (SRS) dataset
narrower: ATACseq (bulk) dataset
narrower: RNAseq (bulk) dataset
narrower: 10X Multiome dataset
narrower: Molecular Cartography dataset
narrower: CosMx Transcriptomics dataset
narrower: Xenium dataset
narrower: MERFISH dataset
narrower: scATACseq dataset
narrower: scRNAseq dataset
narrower: SNARE-seq2 dataset
narrower: 2D Imaging Mass Cytometry dataset
narrower: GeoMx (NGS) dataset
narrower: GeoMx (nCounter) dataset
narrower: Visium (no probes) dataset
narrower: Visium (with probes) dataset
narrower: RNAseq (with probes) dataset
narrower: nanoSPLITS dataset
narrower: Resolve
narrower: Stereo-seq
narrower: Seq-Scope dataset
narrower: DART-FISH
narrower: seqFISH
narrower: MS Lipidomics
narrower: CyTOF
narrower: DBiT-seq dataset
narrower: Singular Genomics G4X dataset
narrower: CosMx Proteomics dataset
narrower: FACS dataset
narrower: Olink dataset
narrower: 4i dataset
narrower: MPLEx dataset
narrower: Pixel-seqV2 dataset
narrower: Visium HD dataset
narrower: COMET dataset

Analyte class
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'analyte class' field within the context of the HuBMAP project.
narrower: Chromatin
narrower: Collagen
narrower: Protein
narrower: DNA
narrower: Metabolite
narrower: Lipid
narrower: Peptide
narrower: RNA
narrower: Polysaccharide
narrower: Fluorochrome
narrower: Endogenous fluorophore
narrower: Nucleic acid + protein
narrower: DNA + RNA
narrower: Saturated lipid
narrower: Unsaturated lipid
narrower: Lipid + metabolite
narrower: RNA + protein
narrower: Lipid + metabolite + protein

Acquisition instrument vendor
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'acquisition instrument vendor' field within the context of the HuBMAP project.
narrower: In house
narrower: Thermo Fisher Scientific
narrower: Leica Microsystems
narrower: Miltenyi Biotec
narrower: Illumina
narrower: Hamamatsu Photonics
narrower: Bruker Corporation
narrower: Cytiva
narrower: Leica Biosystems
narrower: Keyence
narrower: Ionpath
narrower: Standard BioTools
narrower: Zeiss Microscopy
narrower: Andor
narrower: Sciex
narrower: 10x Genomics
narrower: Akoya Biosciences
narrower: Resolve Biosciences
narrower: NanoString Technology
narrower: Waters
narrower: Evident
narrower: BGI Genomics
narrower: Motic
narrower: Huron Digital Pathology
narrower: GE HealthCare
narrower: Vizgen
narrower: Element Biosciences
narrower: Singular Genomics
narrower: Complete Genomics
narrower: 3DHISTECH
narrower: Cytek Biosciences
narrower: Microscopes International
narrower: Revvity Inc.

Acquisition instrument model
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'acquisition instrument model' field within the context of the HuBMAP project.
narrower: In house
narrower: Unknown
narrower: Not applicable
narrower: Illumina NextSeq 500 System
narrower: Illumina NextSeq 550 System
narrower: Illumina HiSeq 2500 System
narrower: Illumina HiSeq 3000/HiSeq 4000 System
narrower: Illumina NovaSeq 6000 System
narrower: Keyence BZ-X710 fluorescent microscope
narrower: Zeiss LSM 710 Confocal Inverted Microscope
narrower: Fluidigm CyTOF Helios mass cytometer
narrower: Sciex QTRAP 5500 mass spectrometer
narrower: Thermo Scientific Q Exactive HF Hybrid Quadrupole-Orbitrap mass spectrometer
narrower: Thermo Scientific Orbitrap Fusion Tribrid mass spectrometer
narrower: Thermo Scientific Orbitrap Fusion Lumos Tribrid mass spectrometer
narrower: Thermo Scientific Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass Spectrometer
narrower: Thermo Scientific Q Exactive GC Orbitrap mass spectrometry
narrower: Thermo Scientific Q Exactive UHMR Hybrid Quadrupole-Orbitrap Mass Spectrometer
narrower: Zeiss Lightsheet Z.1 fluorescence microscope
narrower: Zeiss Axio Scan.Z1 Slide Scanner
narrower: Leica Aperio AT2 Scanner
narrower: Hamamatsu NanoZoomer 2.0-HT Digital slide scanner
narrower: NanoString GeoMx Digital Spatial Profiler
narrower: Biomark HD system
narrower: Hyperion Imaging System
narrower: PhenoImager Fusion
narrower: Andor Zyla 4.2 sCMOS
narrower: Leica SCN400 slide scanner
narrower: Ionpath MIBIscope System
narrower: Illumina NextSeq 2000 System
narrower: Bruker timsTOF fleX with MALDI-2
narrower: GE Healthcare IN Cell Analyzer 2200
narrower: Keyence BZ-X800 fluorescent microscope
narrower: Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer
narrower: Zeiss Axio Observer 5
narrower: Zeiss Axio Observer 3
narrower: Zeiss Axio Observer 7
narrower: Hamamatsu NanoZoomer S210 Digital slide scanner
narrower: Hamamatsu NanoZoomer S360 Digital slide scanner
narrower: Hamamatsu NanoZoomer S60 Digital slide scanner
narrower: Hamamatsu NanoZoomer-SQ Digital slide scanner
narrower: Phenocycler-Fusion
narrower: nanoString CosMx Spatial Molecular Imager
narrower: 10x Genomics Xenium Analyzer
narrower: Zeiss Lightsheet 7
narrower: Resolve Biosciences Molecular Cartography
narrower: Illumina NovaSeq X Plus
narrower: Illumina NovaSeq X
narrower: Leica STELLARIS 5 microscope
narrower: Olympus VS200 Slide Scanner
narrower: 3DHISTECH Pannoramic MIDI II Scanner
narrower: MGI DNBSEQ-T7 Genetic Sequencer
narrower: MoticEasyScan One
narrower: Leica DM6 B Upright Microscope
narrower: TissueScope LE Slide Scanner
narrower: EVOS M7000 Imaging System
narrower: Leica Aperio CS2 Scanner
narrower: Keyence BZ-X810 microscope
narrower: Vizgen MERSCOPE Ultra
narrower: Standard Biotools CyTOF XT mass cytometer
narrower: Element AVITI24 system
narrower: Bruker timsTOF Ultra mass spectrometer
narrower: Bruker timsTOF Ultra 2 mass spectrometer
narrower: Bruker timsTOF SCP mass spectrometer
narrower: Bruker timsTOF HT mass spectrometer
narrower: Bruker timsTOF Pro mass spectrometer
narrower: Bruker timsTOF Pro 2 mass spectrometer
narrower: Fluidigm CyTOF 2 mass cytometer
narrower: Leica DMi8 Inverted Microscope
narrower: Singular Genomics G4X Spatial Sequencer
narrower: Bruker timsTOF FleX
narrower: Cytek Northern Lights flow cytometer
narrower: Zeiss Axio Zoom.V16 for Biology
narrower: Bruker solariX
narrower: Microscopes International uScopeHXII-20 microscope
narrower: Fluidigm Juno Targeted DNA Sequencing Library Preparation System
narrower: Leica Cell DIVE Multiplex Imaging Solution System

Time since acquisition instrument calibration unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'time since acquisition instrument calibration unit' field within the context of the HuBMAP project.
narrower: day
narrower: month
narrower: year

Stain name
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'stain name' field within the context of the HuBMAP project.
narrower: Alcian Blue stain with Periodic acid-Schiff
narrower: Hematoxylin and eosin stain
narrower: Luxol fast blue/Cresyl violet stain
narrower: Periodic acid-Schiff stain
narrower: Sudan black B stain
narrower: Trichrome stain
narrower: Hematoxylin and 3,3′-Diaminobenzidine stain
narrower: Fluorophores

Stain technique
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'stain technique' field within the context of the HuBMAP project.
narrower: Not applicable
narrower: Regressive staining
narrower: Modified progressive staining
narrower: Progressive staining

Preparation instrument vendor
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'preparation instrument vendor' field within the context of the HuBMAP project.
narrower: In house
narrower: Not applicable
narrower: Thermo Fisher Scientific
narrower: Hamamatsu Photonics
narrower: Leica Biosystems
narrower: Ionpath
narrower: 10x Genomics
narrower: HTX Technologies
narrower: Akoya Biosciences
narrower: SunChrom
narrower: Roche Diagnostics

Preparation instrument model
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'preparation instrument model' field within the context of the HuBMAP project.
narrower: Not applicable
narrower: Customize
narrower: 10x Genomics Chromium Plus Genetic Analyzer
narrower: HTX Sublimator
narrower: HTX M3+ Sprayer
narrower: HTX TM-Sprayer
narrower: HTX M5 Sprayer
narrower: Hamamatsu NanoZoomer S210 Digital slide scanner
narrower: Hamamatsu NanoZoomer S360 Digital slide scanner
narrower: Hamamatsu NanoZoomer S60 Digital slide scanner
narrower: SunCollect MALDI Sprayer
narrower: Leica Autostainer ST5010 XL
narrower: 10x Genomics Chromium iX Single Cell Analyzer
narrower: 10x Genomics Chromium X Single Cell Analyzer
narrower: Visium CytAssist
narrower: Leica ST5020 Multistainer Slide Stainer
narrower: EVOS M7000 Imaging System
narrower: Ventana Discovery Ultra
narrower: 10x Genomics Chromium Connect system

Tile configuration
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'tile configuration' field within the context of the HuBMAP project.
narrower: Not applicable
narrower: Snake-by-columns
narrower: Snake-by-rows
narrower: Column-by-column
narrower: Row-by-row

Scan direction
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'scan direction' field within the context of the HuBMAP project.
narrower: Not applicable
narrower: Left-and-down
narrower: Left-and-up
narrower: Right-and-down
narrower: Right-and-up

Total run time unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'total run time unit' field within the context of the HuBMAP project.
narrower: minute
narrower: hour

Laterality
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'laterality' field within the context of the HuBMAP project.
narrower: Right
narrower: Left
narrower: Not applicable
narrower: Midline

Organ condition
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'organ condition' field within the context of the HuBMAP project.
narrower: Healthy
narrower: Diseased
narrower: Unknown

Perfusion solution
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'perfusion solution' field within the context of the HuBMAP project.
narrower: Unknown
narrower: None
narrower: Miltenyi Tissue Preservation Buffer
narrower: University of Wisconsin Solution
narrower: Histidine-Tryptophan-Ketoglutarate Solution
narrower: Belzer MPS/KPS
narrower: Perfadex Plus

Transport solution
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'transport solution' field within the context of the HuBMAP project.
narrower: Roswell Park Memorial Institute 1640 Medium
narrower: Unknown
narrower: Dulbecco's Modified Eagle Medium
narrower: None
narrower: Neutral buffered formalin
narrower: Phosphate buffered saline solution
narrower: Miltenyi Tissue Preservation Buffer
narrower: University of Wisconsin Solution
narrower: Histidine-Tryptophan-Ketoglutarate Solution
narrower: Belzer MPS/KPS
narrower: Saline (Buffered)
narrower: Perfadex Plus

Warm ischemic time unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'warm ischemic time unit' field within the context of the HuBMAP project.
narrower: minute
narrower: hour

Cold ischemic time unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'cold ischemic time unit' field within the context of the HuBMAP project.
narrower: minute
narrower: hour

Weight unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'weight unit' field within the context of the HuBMAP project.
narrower: kilogram
narrower: gram
narrower: milligram

Height unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'height unit' field within the context of the HuBMAP project.
narrower: centimeter
narrower: millimeter

Width unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'width unit' field within the context of the HuBMAP project.
narrower: centimeter
narrower: millimeter

Length unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'length unit' field within the context of the HuBMAP project.
narrower: centimeter
narrower: millimeter

Library input amount unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'library input amount unit' field within the context of the HuBMAP project.
narrower: nanogram
narrower: microliter

Library output amount unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'library output amount unit' field within the context of the HuBMAP project.
narrower: nanogram
narrower: microliter

Library concentration unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'library concentration unit' field within the context of the HuBMAP project.
narrower: nanomolar
narrower: nanogram per microliter
narrower: picogram per microliter

Library layout
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'library layout' field within the context of the HuBMAP project.
narrower: paired-end library
narrower: single-end library

Library preparation kit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'library preparation kit' field within the context of the HuBMAP project.
narrower: Customize
narrower: 10x Genomics; Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns; PN 1000283
narrower: 10x Genomics; Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxns; PN 1000285
narrower: 10x Genomics; Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3, 4 rxns; PN 1000092
narrower: 10x Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 rxns; PN 1000184
narrower: 10x Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 1 slides, 4 rxns; PN 1000187
narrower: 10x Genomics; Chromium Single Cell 3' Library & Gel Bead Kit, 4 rxns; PN 120267
narrower: 10x Genomics; Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome, 1 slides, 4 rxns; PN 1000338
narrower: 10x Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Human Transcriptome, 6.5mm, 4 rxns; PN 1000520
narrower: 10x Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Human Transcriptome, 11 mm, 2 rxns; PN 1000522
narrower: 10x Genomics; Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, 16 rxns; PN 1000121
narrower: 10x Genomics; Chromium Next GEM Single Cell 3' HT Kit v3.1, 48 rxns; PN 1000348
narrower: 10x Genomics; Chromium Next GEM Single Cell 3' HT Kit v3.1, 8 rxns; PN 1000370
narrower: 10x Genomics; Chromium Next GEM Single Cell 3' Kit v3.1, 16 rxns; PN 1000268
narrower: 10x Genomics; Chromium Next GEM Single Cell 3' Kit v3.1, 4 rxns; PN 1000269
narrower: 10x Genomics; Chromium Next GEM Single Cell 5' Kit v2, 16 rxns; PN 1000263
narrower: 10x Genomics; Chromium Next GEM Single Cell 5' Kit v2, 4 rxns; PN 1000265
narrower: Parse Biosciences; Evercode WT v2 Kit, 48 rxns; PN ECW02030
narrower: Parse Biosciences; Evercode WT Mini v2 Kit, 12 rxns; PN ECW02010
narrower: Illumina; TruSeq Stranded mRNA Library Prep (48 samples); PN 20020594
narrower: Illumina; TruSeq Stranded mRNA Library Prep (96 samples); PN 20020595
narrower: 10x Genomics; Visium Spatial for FFPE Gene Expression Kit, Mouse Transcriptome, 4 rxns; PN 1000339
narrower: 10x Genomics; Chromium Next GEM Automated Single Cell 5' Kit v2, 24 rxns; PN 1000290
narrower: 10x Genomics; Chromium Next GEM Automated Single Cell 5' Kit v2, 4 rxns; PN 1000298
narrower: 10x Genomics; Automated Library Construction Kit, 24 rxns; PN 1000428
narrower: 10x Genomics; Chromium Next GEM Single Cell Fixed RNA Hybridization & Library Kit, 4 rxns; PN 1000415
narrower: New England BioLabs; NEBNext Ultra II RNA Library Prep Kit for Illumina; PN E7770
narrower: 10x Genomics; Chromium GEM-X Single Cell 5' Kit v3, 16 rxns; PN 1000699
narrower: 10x Genomics; Library Construction Kit C, 4 rxns; PN 1000689
narrower: 10x Genomics; Library Construction Kit C, 16 rxns; PN 1000694
narrower: 10x Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Mouse Transcriptome, 6.5mm, 4 rxns; PN 1000521
narrower: 10x Genomics; Library Construction Kit, 16 rxns; PN 1000190
narrower: 10x Genomics; Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, 16 rxns; PN 1000075
narrower: 10x Genomics; Chromium Next GEM Single Cell 5' HT Kit v2, 8 rxns; PN 1000374
narrower: 10x Genomics; Chromium Next GEM Single Cell 5' HT Kit v2, 48 rxns; PN 1000356
narrower: 10x Genomics; Chromium Single Cell ATAC Library & Gel Bead Kit, 16 rxns; PN 1000110
narrower: 10x Genomics; Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, 16 rxns; PN 1000175
narrower: 10x Genomics; Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit, 16 rxns; PN 1000414

Sample indexing kit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'sample indexing kit' field within the context of the HuBMAP project.
narrower: Not applicable
narrower: Customize
narrower: 10x Genomics; Single Index Kit N, Set A, 96 rxns; PN 1000212
narrower: 10x Genomics; Dual Index Kit TT, Set A, 96 rxns; PN 1000215
narrower: 10x Genomics; Dual Index Kit TS, Set A; PN 1000251
narrower: Parse Biosciences; Fragmentation Reagents; PN WX100
narrower: Parse Biosciences; UDI Plate - WT; PN UDI1001
narrower: Illumina; TruSeq RNA Single Indexes Set A (12 Indexes, 48 Samples); PN 20020492
narrower: Illumina; TruSeq RNA Single Indexes Set B (12 Indexes, 48 Samples); PN 20020493
narrower: Illumina; TruSeq RNA CD Index Plate (96 Indexes, 96 Samples); PN 20019792
narrower: Illumina; IDT for Illumina - TruSeq RNA UD Indexes v2 (96 Indexes, 96 Samples); PN 20040871
narrower: Integrated DNA Technologies: Custom DNA Oligos
narrower: NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-AB
narrower: NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-CD
narrower: NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-EF
narrower: NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-GH
narrower: 10x Genomics; Chromium i7 Sample Index Plate, 96 rxns; PN 220103
narrower: 10x Genomics; Chromium i7 Multiplex Kit, 96 rxns; PN 120262
narrower: 10x Genomics; Chromium i7 Multiplex Kit N, Set A, 96 rxn; PN 1000084

Barcode read
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'barcode read' field within the context of the HuBMAP project.
narrower: Read pair 1
narrower: Read pair 2
narrower: Not applicable

UMI read
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'UMI read' field within the context of the HuBMAP project.
narrower: Read pair 1
narrower: Read pair 2
narrower: Not applicable

Sequencing reagent kit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'sequencing reagent kit' field within the context of the HuBMAP project.
narrower: Customize
narrower: Illumina; HiSeq 3000/4000 PE Cluster Kit PE-410-1001; PN 1000283
narrower: Illumina; NextSeq 500/550 Hi Output v2.5 Kit (150 Cycles); PN 20024907
narrower: Illumina; NovaSeq 6000 SP Reagent v1.5 Kit (100 Cycles); PN 20028401
narrower: Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (100 Cycles); PN 20028319
narrower: Illumina; NovaSeq 6000 S2 Reagent v1.5 Kit (100 Cycles); PN 20028316
narrower: Illumina; NovaSeq 6000 S4 Reagent v1.5 Kit (200 Cycles); PN 20028313
narrower: Illumina; NovaSeq X Series 10B Reagent Kit (300 Cycle); PN 20085594
narrower: Illumina; NovaSeq X Series 10B Reagent Kit (200 Cycle); PN 20085595
narrower: Illumina; NovaSeq X Series 10B Reagent Kit (100 Cycle); PN 20085596
narrower: Illumina; NovaSeq X Series 1.5B Reagent Kit (100 Cycle); PN 20104703
narrower: Illumina; NovaSeq X Series 1.5B Reagent Kit (200 Cycle); PN 20104704
narrower: Illumina; NovaSeq X Series 1.5B Reagent Kit (300 Cycle); PN 20104705
narrower: Illumina; NovaSeq 6000 S1 Reagent Kit (200 Cycles); PN 20012864
narrower: Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (300 Cycles); PN 20028317
narrower: Illumina; NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles); PN 20028312
narrower: Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (100 Cycles); PN 20046811
narrower: Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (200 Cycles); PN 20046812
narrower: Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (300 Cycles); PN 20046813
narrower: Illumina; NextSeq 2000 P3 Reagent Kit (300 Cycles); PN 20040561
narrower: Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (200 Cycles); PN 20028318
narrower: Illumina; NextSeq 2000 P3 Reagents Kit (100 Cycles); PN 20040559
narrower: Illumina; NextSeq 500/550 Mid Output v2.5 Kit (150 Cycles); PN 20024904
narrower: Illumina; NextSeq 500/550 Hi Output v2.5 Kit (75 Cycles); PN 20024906
narrower: Illumina; NovaSeq X Series 25B Reagent Kit (300 Cycle); PN 20104706
narrower: Element Biosciences; AVITI 2x75 Sequencing Kit Cloudbreak FS High Output (184 Cycles); PN 860-00015
narrower: Illumina; NovaSeq 6000 SP Reagent v1.5 Kit (300 Cycles); PN 20028400
narrower: Illumina; NovaSeq X Series 25B Reagent Kit (100 Cycle); PN 20125967
narrower: Illumina; NovaSeq X Series 25B Reagent Kit (200 Cycle); PN 20125968

Transposition reagent kit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'transposition reagent kit' field within the context of the HuBMAP project.
narrower: Not applicable
narrower: Customize
narrower: 10x Genomics; Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns; PN 1000283
narrower: 10x Genomics; Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxns; PN 1000285
narrower: 10x Genomics; Chromium Single Cell ATAC Library & Gel Bead Kit, 16 rxns; PN 1000110
narrower: 10x Genomics; Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, 16 rxns; PN 1000175
narrower: Illumina; Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit; PN 20034197

Transposition method
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'transposition method' field within the context of the HuBMAP project.
narrower: Customize
narrower: Single-cell ATAC-seq
narrower: Bulk assay for transposase-accessible chromatin using sequencing
narrower: Single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing

Assay input unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'assay input unit' field within the context of the HuBMAP project.
narrower: microgram

Assay input entity
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'assay input entity' field within the context of the HuBMAP project.
narrower: tissue (bulk)
narrower: single cell
narrower: single nucleus
narrower: spot
narrower: area of interest

Preparation instrument kit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'preparation instrument kit' field within the context of the HuBMAP project.
narrower: Customize
narrower: 10x Genomics; Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns; PN 1000283
narrower: 10x Genomics; Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxns; PN 1000285
narrower: 10x Genomics; Visium FFPE Reagent Kit v2-Small; PN 1000436
narrower: 10x Genomics; Chromium Next GEM Chip Q Single Cell Kit, 16 rxns; PN 1000422
narrower: 10x Genomics; Chromium Next GEM Chip K Single Cell Kit, 48 rxns; PN 1000286
narrower: 10x Genomics; Chromium Next GEM Chip K Single Cell Kit, 16 rxns; PN 1000287
narrower: 10x Genomics; Chromium Next GEM Chip K Automated Single Cell Kit, 48 rxns; PN 1000289
narrower: 10x Genomics; Chromium Next GEM Chip G Single Cell Kit, 48 rxns; PN 1000120
narrower: 10x Genomics; Chromium Next GEM Chip G Single Cell Kit, 16 rxns; PN 1000127
narrower: 10x Genomics; Chromium GEM-X Single Cell 3' Kit v4, 16 rxns; PN 1000691
narrower: 10x Genomics; Chromium Single Cell B Chip Kit, 16 rxns; PN 1000074
narrower: 10x Genomics; Chromium Chip E Single Cell ATAC Kit, 48 rxns; PN 1000155

Amount of input analyte unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'amount of input analyte unit' field within the context of the HuBMAP project.
narrower: microgram
narrower: nanogram

Mapped area unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'mapped area unit' field within the context of the HuBMAP project.
narrower: square millimeter
narrower: square micrometer

Spot size unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'spot size unit' field within the context of the HuBMAP project.
narrower: square millimeter
narrower: square micrometer

Spot spacing unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'spot spacing unit' field within the context of the HuBMAP project.
narrower: micrometer

Permeabilization time unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'permeabilization time unit' field within the context of the HuBMAP project.
narrower: minute

RNA probe panel
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'RNA probe panel' field within the context of the HuBMAP project.
narrower: Not applicable
narrower: Customize

MS ionization technique
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'mass spectrometry ionization technique' field within the context of the HuBMAP project.
narrower: Laser ablation
narrower: Electrospray ionization
narrower: Matrix-assisted laser desorption ionization
narrower: Laser desorption ionization
narrower: Desorption electrospray ionization
narrower: Nanospray desorption electrospray ionization assay
narrower: MALDI-2
narrower: SIMS-C60
narrower: SIMS-H20
narrower: Heated electrospray ionization
narrower: Nano electrospray ionization

Mass analysis polarity
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'mass analysis polarity' field within the context of the HuBMAP project.
narrower: Negative ion mode
narrower: Positive ion mode
narrower: Negative and positive ion mode

Ion mobility
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'ion mobility' field within the context of the HuBMAP project.
narrower: Thermal Ionization Mass Spectrometry
narrower: Travelling Wave Ion Mobility Spectrometry
narrower: Field Asymmetric Ion Mobility Spectrometry
narrower: Dispersive or Drift Tube Ion Mobility Spectrometry
narrower: Structures for Lossless Ion Manipulations
narrower: Cyclic Ion Mobility Spectrometry

MS scan mode
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'mass spectrometry scan mode' field within the context of the HuBMAP project.
narrower: MS1
narrower: MS2
narrower: MS3

Matrix deposition method
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'matrix deposition method' field within the context of the HuBMAP project.
narrower: Not applicable
narrower: Robotic spotting
narrower: Electrospray deposition
narrower: Robotic spraying
narrower: Sublimation

Preparation matrix
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'preparation matrix' field within the context of the HuBMAP project.
narrower: 4-(dimethylamino)cinnamic acid
narrower: 2,5-Dihydroxybenzoic acid
narrower: 2',5'-Dihydroxyacetophenone
narrower: N-(1-naphthyl)ethylenediamine dihydrochloride
narrower: alpha-cyano-4-hydroxycinnamic acid
narrower: 9-aminoacridine
narrower: sinapic acid
narrower: DAN (1,5-diaminonapthalene)
narrower: MAPCA (methyl 3-(4-aminophenyl)-2-cyanoacrylate)

Desorption solvent
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'desorption solvent' field within the context of the HuBMAP project.
narrower: Methanol:Water (MeOH:H2O)
narrower: Methanol:Ethanol (MeOH:EtOH)
narrower: Acetonitrile:Water (ACN:H2O)
narrower: Acetonitrile:Dimethylformamide (ACN:DMF)
narrower: Ethanol:Water (EtOH:H2O)
narrower: Ethanol:Dimethylformamide (EtOH:DMF)

Desorption solvent flow rate unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'desorption solvent flow rate unit' field within the context of the HuBMAP project.
narrower: microliters per minute
narrower: nL/min

Data collection mode
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'desorption solvent flow rate unit' field within the context of the HuBMAP project.
narrower: Data-Dependent Acquisition
narrower: Data-Independent Acquisition
narrower: Selected Reaction Monitoring
narrower: Parallel Reaction Monitoring

LC instrument vendor
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'liquid chromatography instrument vendor' field within the context of the HuBMAP project.
narrower: In house
narrower: Thermo Fisher Scientific
narrower: Agilent Technologies
narrower: Bruker Corporation
narrower: Sciex
narrower: Waters
narrower: Evosep
narrower: Shimadzu

LC column vendor
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'liquid chromatography column vendor' field within the context of the HuBMAP project.
narrower: In house
narrower: Thermo Fisher Scientific
narrower: MilliporeSigma
narrower: Agilent Technologies
narrower: Bruker Corporation
narrower: Waters
narrower: Evosep
narrower: IonOpticks

LC column length unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'liquid chromatography column length unit' field within the context of the HuBMAP project.
narrower: centimeter
narrower: millimeter
narrower: micrometer

LC temperature unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'liquid chromatography temperature unit' field within the context of the HuBMAP project.
narrower: degree Celsius

LC inner diameter unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'liquid chromatography inner diameter unit' field within the context of the HuBMAP project.
narrower: centimeter
narrower: millimeter
narrower: micrometer

LC flow rate unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'liquid chromatography flow rate unit' field within the context of the HuBMAP project.
narrower: nL/min
narrower: mL/min

LC gradient unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'liquid chromatography gradient unit' field within the context of the HuBMAP project.
narrower: minute

Spatial sampling technique
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'spatial sampling technique' field within the context of the HuBMAP project.
narrower: Laser Capture Microdissection
narrower: Nanodroplet Processing in One pot for Trace Samples
narrower: Liquid Extraction Surface Analysis
narrower: Microscale Liquid Extraction Surface Analysis
narrower: Microscale Pots for Analysis of Transferred Samples
narrower: nanoSPLITS

Spatial sampling type
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'spatial sampling type' field within the context of the HuBMAP project.
narrower: Profiling
narrower: Imaging

Target retrieval incubation time unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'target retrieval incubation time unit' field within the context of the HuBMAP project.
narrower: minute

ProteinaseK incubation time unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'proteinasek incubation time unit' field within the context of the HuBMAP project.
narrower: minute

Area normalized ion dose unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'area normalized ion dose unit" field within the context of the HuBMAP project.
narrower: nA*hr/mm2

Pixel dwell time unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'pixel dwell time unit' field within the context of the HuBMAP project.
narrower: millisecond

Ablation frequency unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'ablation frequency unit' field within the context of the HuBMAP project.
narrower: hertz

Antibody concentration unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'antibody concentration unit' field within the context of the HuBMAP project.
narrower: microgram per milliliter

ROI segmentation strategy
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'ROI segmentation strategy' field within the context of the HuBMAP project.
narrower: Automated segmentation
narrower: Manual segmentation

Probe hybridization time unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'Probe hybridization time unit' field within the context of the HuBMAP project.
narrower: minute
narrower: hour

Oligo probe panel
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'Oligo probe panel' field within the context of the HuBMAP project.
narrower: Customize
narrower: 10x Genomics; Visium Human Transcriptome Probe Kit v2 - Small; PN 1000466
narrower: 10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome, 4 rxns x 1 BC; PN 1000474
narrower: 10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome 4 rxns x 4 BC; PN 1000475
narrower: 10x Genomics; Visium Human Transcriptome Probe Kit-Small; PN 1000363
narrower: 10x Genomics; Visium Mouse Transcriptome Probe Kit - Small; PN 1000365
narrower: NanoString Technologies; GeoMx Human Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-HuWTA-4
narrower: NanoString Technologies; GeoMx Mouse Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-MsWTA-4
narrower: 10x Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 64 rxns; PN 1000456
narrower: 10x Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 16 rxns; PN 1000420
narrower: 10x Genomics; Visium Human Transcriptome Probe Kit-Large; PN 1000364
narrower: 10x Genomics; Chromium Next GEM Single Cell Fixed RNA Mouse Transcriptome Probe Kit, 64 rxns; PN 1000492
narrower: 10x Genomics; Xenium Human Multi-Tissue and Cancer Panel v1; PN 1000626
narrower: 10x Genomics; Xenium Prime 5K Human Pan Tissue & Pathways Panel; PN 1000724
narrower: NanoString Technologies; CosMx Human Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-H-USCP-1KP-R
narrower: 10x Genomics; Visium Mouse Transcriptome Probe Kit v2.0 - Small; PN 1000667
narrower: NanoString Technologies; CosMx Human Immuno-Oncology Panel (Protein, 64 Plex); PN CMX-H-IOP-64P-P
narrower: NanoString Technologies; CosMx Mouse Neuroscience Panel (Protein, 64 Plex); PN CMX-M-Neuro-64P-P
narrower: 10x Genomics; Xenium Mouse Multi-Tissue Atlassing Panel; PN 1000627
narrower: 10x Genomics; Xenium Human Lung Gene Expression Panel; PN 1000601
narrower: 10x Genomics; Xenium Custom Gene Expression Panel, (51-100 genes); PN 1000561
narrower: 10x Genomics; Xenium Custom Gene Expression Panel (up to 50 genes); PN 1000464
narrower: 10x Genomics; Xenium Human Colon Gene Expression Panel; PN 1000642
narrower: NanoString Technologies; CosMx Mouse Neuroscience Panel (RNA, 1000 Plex); PN CMX-M-NEUP-R
narrower: NanoString Technologies; CosMx Hs WTX RNA Panel Kit, 2 slides: PN 121500047
narrower: NanoString Technologies; CosMx Hs Univ Cell (RNA, 1000 Plex); PN 121500002
narrower: NanoString Technologies; CosMx Human 6K Discovery Panel (RNA, 6175 Plex); PN 121500041
narrower: NanoString Technologies; CosMx Mouse Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-M-USCP-1KP-R
narrower: 10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome 16 rxns x 16 BC; PN 1000547
narrower: 10x Genomics; GEM-X Flex Human Transcriptome Probe Kit, 16 samples; PN 1000785
narrower: NanoString Technologies; GeoMx Human IO Proteome Atlas, 4 slides; PN 121300160
narrower: 10x Genomics; Xenium Human Skin Gene Expression Panel; PN 1000643

Derived dataset type
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'Derived dataset type' field within the context of the HuBMAP project.
narrower: Segmentation Mask dataset
narrower: Object x Analyte dataset

Clonality
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'Clonality' field within the context of the HuBMAP project.
narrower: monoclonal
narrower: polyclonal

Antibody reagent kit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'antibody reagent kit' field within the context of the HuBMAP project.
narrower: Customize
narrower: Standard BioTools; Maxpar Phosphoprotein Staining Kit; PN 201604
narrower: Standard BioTools; Maxpar Nuclear Antigen Staining Kit; PN 201603
narrower: Standard BioTools; Maxpar Cytoplasmic/Secreted Antigen Staining Kit; PN 201602
narrower: Standard BioTools; Maxpar Cell Surface Staining Kit; PN 201601

Viability reagent kit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'viability reagent kit' field within the context of the HuBMAP project.
narrower: None
narrower: Customize
narrower: Standard BioTools; Cell-ID Cisplatin 100 uL; PN 201064
narrower: Standard BioTools; Cell-ID Cisplatin-194Pt 100 uL; PN 201194
narrower: Standard BioTools; Cell-ID Cisplatin-195Pt 100 uL; PN 201195
narrower: Standard BioTools; Cell-ID Cisplatin-196Pt 100 uL; PN 201196
narrower: Standard BioTools; Cell-ID Cisplatin-198Pt 100 uL; PN 201198
narrower: Standard BioTools; Cell-ID Intercalator-103Rh 500 um; PN 201103A
narrower: Standard BioTools; Cell-ID Intercalator-103Rh 2,000 um; PN 201103B
narrower: Sigma Aldrich; Cisplatin 25mg; PN P4394

Instrument calibration bead kit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'instrument calibration bead kit' field within the context of the HuBMAP project.
narrower: None
narrower: Customize
narrower: Standard BioTools; CyTOF Calibration Beads; PN 201073
narrower: Standard BioTools; EQ Four Element Calibration Beads 100 mL; PN 201078
narrower: Standard BioTools; EQ Six Element Calibration Beads 100 mL; PN 201245

Loaded cell concentration unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'loaded cell concentration unit' field within the context of the HuBMAP project.
narrower: cells/mL

Chemistry kit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'Chemistry kit' field within the context of the HuBMAP project.
narrower: Customize

Capture area width unit
type: NamedIndividual
type: Concept
narrower: millimeter

Capture area height unit
type: NamedIndividual
type: Concept
narrower: millimeter

Spatial discretization method
type: NamedIndividual
type: Concept
narrower: Cell segmentation
narrower: Square binning
narrower: Hexagonal binning

Signal quenching method
type: NamedIndividual
type: Concept
narrower: Photobleaching
narrower: Enzymatic cleavage

Sex
type: NamedIndividual
type: Concept
definition: Sex of the source organism
narrower: Male
narrower: Female

Euthanization method
type: NamedIndividual
type: Concept
definition: If the source was euthanized, select the method of euthanization.
narrower: Other
narrower: Decapitation
narrower: Intravenous anesthetic euthanasia
narrower: Cervical dislocation
narrower: Carbon dioxide inhalant euthanasia
narrower: Hypothermia
narrower: Rapid freezing
narrower: Inhaled anesthetic euthanasia

Hypothermia
type: NamedIndividual
type: Concept
broader: Euthanization method
definition: Organism was euthanized by gradual cooling to induce deep anesthesia and subsequent euthanasia.

Rapid freezing
type: NamedIndividual
type: Concept
broader: Euthanization method
definition: Organism was euthanized by rapid freezing in liquid nitrogen.

Inhaled anesthetic euthanasia
type: NamedIndividual
type: Concept
broader: Euthanization method
definition: Organism was euthanized by inhalation of anesthetic.

Room health status
type: NamedIndividual
type: Concept
definition: A description of the pathogen and opportunist exclusion level of the room where the source is housed.
narrower: Other
narrower: Pathogen free
narrower: Pathogen and opportunist free

Pathogen free
type: NamedIndividual
type: Concept
broader: Room health status
definition: Organism housed in a room free of pathogens.

Pathogen and opportunist free
type: NamedIndividual
type: Concept
broader: Room health status
definition: Organism housed in a room free of pathogens and opportunistic organisms.

Rack setup
type: NamedIndividual
type: Concept
definition: The rack setup type in which the source is housed.
narrower: Other
narrower: Biocontainment
narrower: Ventilated
narrower: Micro-Isolator
narrower: Conventional

Biocontainment
type: NamedIndividual
type: Concept
broader: Rack setup
definition: Organism housed in biocontainment cages designed to prevent the spread of pathogens within and between groups of individual organisms.

Ventilated
type: NamedIndividual
type: Concept
broader: Rack setup
definition: Organism housed in ventilated cages providing filtered air directly to the cage.

Micro-Isolator
type: NamedIndividual
type: Concept
broader: Rack setup
definition: Organism housed in microisolator cages to protect animals against contamination from the outside environment.

Conventional
type: NamedIndividual
type: Concept
broader: Rack setup
definition: Organism housed in cages where the housing environment is not isolated from the animal housing room.

Light cycle
type: NamedIndividual
type: Concept
definition: The light cycle in the room where the source is housed.
narrower: Standard/default
narrower: Other
narrower: Longer photoperiods
narrower: Reverse light cycles

Longer photoperiods
type: NamedIndividual
type: Concept
broader: Light cycle
definition: Organism housed with photoperiods longer that standard/default light cycle.

Reverse light cycles
type: NamedIndividual
type: Concept
broader: Light cycle
definition: Organism housed with the lights OFF during the daytime and ON during the nighttime.

Bedding
type: NamedIndividual
type: Concept
definition: The type of cage bedding in the cage where the source is housed.
narrower: Aspen chip bedding
narrower: Aspen shaving bedding
narrower: Corn cob bedding
narrower: Pine chip bedding
narrower: Pine shaving bedding
narrower: Other
narrower: 1/4-inch pelleted cellulose
narrower: Refined virgin diced cellulose
narrower: Non-contact cage board
narrower: Wire mesh

1/4-inch pelleted cellulose
type: NamedIndividual
type: Concept
broader: Bedding
definition: Organism housed with bedding made from 1/4-inch pelleted cellulose.

Refined virgin diced cellulose
type: NamedIndividual
type: Concept
broader: Bedding
definition: Organism housed with bedding made from refined virgin diced cellulose.

Non-contact cage board
type: NamedIndividual
type: Concept
broader: Bedding
definition: Organism housed with bedding made from one of a variety of cage boards.

Wire mesh
type: NamedIndividual
type: Concept
broader: Bedding
definition: Organism housed with bedding made from wire mesh suspended above a collection pan.

Cage enhancements
type: NamedIndividual
type: Concept
definition: Environmental enrichments present in the source’s cage.
narrower: Other
narrower: Nestlets
narrower: Nest boxes/shelters
narrower: Shelter tubes
narrower: Wooden chew sticks
narrower: Nylon bones

Nestlets
type: NamedIndividual
type: Concept
broader: Cage enhancements
definition: Organism housed with nesting material made from paper or cotton fibers.

Nest boxes/shelters
type: NamedIndividual
type: Concept
broader: Cage enhancements
definition: Organism housed with man-made enclosures for nesting.

Shelter tubes
type: NamedIndividual
type: Concept
broader: Cage enhancements
definition: Organism housed with man-made tubes for nesting.

Wooden chew sticks
type: NamedIndividual
type: Concept
broader: Cage enhancements
definition: Organism housed with wooden chew sticks for chewing.

Nylon bones
type: NamedIndividual
type: Concept
broader: Cage enhancements
definition: Organism housed with nylon bones for chewing.

Imaging instrument vendor
type: NamedIndividual
type: Concept
definition: An image capture instrument is the device that contains the image detection hardware and signal processing software.
narrower: GE HealthCare

Imaging instrument model
type: NamedIndividual
type: Concept
definition: Manufacturers of an acquisition instrument may offer various versions (models) of equipment with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.
narrower: Discovery MR750 3.0T MR system

Image width unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'image width unit' field.
narrower: millimeter
narrower: micrometer

Image height unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'image height unit' field.
narrower: millimeter
narrower: micrometer

Pixel physical size width unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'pixel physical size width unit' field.
narrower: millimeter
narrower: micrometer
narrower: nanometer

Pixel physical size height unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'pixel physical size height unit' field.
narrower: millimeter
narrower: micrometer
narrower: nanometer

Pixel physical size depth unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'pixel physical size depth unit' field.
narrower: millimeter
narrower: micrometer
narrower: nanometer

Spacing between slices unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'spacing between slices unit' field or the unit of incremental distance between image slices.
narrower: millimeter
narrower: micrometer
narrower: nanometer

Imaging frequency unit
type: NamedIndividual
type: Concept
definition: This is a set of permissible values for 'imaging frequency unit' field or the unit of the frequencu at which the imaging device is operating.
narrower: Hertz
narrower: Kilohertz
narrower: Megahertz

Modality
type: NamedIndividual
type: Concept
definition: Type of device, process or method used to acquire or derive data.
narrower: Magnetic resonance