The graph representation of the HuBMAP Research Attributes Value Set dataset.
Sample ID
Unique HuBMAP or SenNet identifier for the sample assigned by the ingest portal.
sample_id
Source storage duration value
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.
source_storage_duration_value
Source storage duration unit
Time unit.
source_storage_duration_unit
Preparation medium
The media used during preparation of the sample.
preparation_medium
Preparation condition
The condition under which the preparation occurred, such as whether the sample was placed in dry ice during the preparation.
preparation_condition
Processing time value
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.
processing_time_value
Processing time unit
Time unit
processing_time_unit
Storage medium
The medium in which the sample is stabilized for storage.
storage_medium
Storage method
The method by which the sample was stored, after preparation and before the assay was performed.
storage_method
Quality criteria
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".
quality_criteria
Histological report
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.)
histological_report
Thickness value
Thickness of a tissue section
thickness_value
Thickness unit
thickness_unit
Section index number
The index number for the section if the sample is a single section.
section_index_number
Area value
The area of a tissue section.
area_value
Area unit
area_unit
Notes
Miscellaneous details about the sample, not captured in the existing metadata fields.
notes
Metadata schema ID
The ID that uniquely identifies the version of the metadata schema being used.
metadata_schema_id
Volume value
The volume of an entity
volume_value
Volume unit
The unit of measurment for volume.
volume_unit
Tissue weight value
Weight of a tissue block or the piece of tissue.
tissue_weight_value
Tissue weight unit
The unit of measurement for tissue weight.
tissue_weight_unit
Pathology distance value
If surgical sample, how far from the pathology was the sample obtained. Typically a number of centimeters. Leave blank if not applicable or unknown.
pathology_distance_value
Pathology distance unit
Distance unit.
pathology_distance_unit
Suspension entity type
The type of single cell entity derived from isolation protocol.
suspension_entity_type
Suspension entity count
Total number of cell/nuclei yielded post dissociation and enrichment.
suspension_entity_count
Is suspension enriched?
Was the cell/nuclei population enriched?
is_suspension_enriched
Suspension enriched target
If the suspension was enriched, then this is the target of the enrichment.
suspension_enriched_target
Lab ID
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.
lab_id
Dataset type
The specific main type of assay being executed.
dataset_type
Analyte class
Analytes are the target molecules being measured with the assay.
analyte_class
Is targeted?
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. The CODEX analyte is protein.
is_targeted
Acquisition instrument vendor
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.
acquisition_instrument_vendor
Acquisition instrument model
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.
acquisition_instrument_model
Time since acquisition instrument calibration value
The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture.
time_since_acquisition_instrument_calibration_value
Time since acquisition instrument calibration unit
The time since acquisition instrument calibration units
time_since_acquisition_instrument_calibration_unit
Contributors path
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.
contributors_path
Data path
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.
data_path
Is image preprocessing required?
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).
is_image_preprocessing_required
Stain name
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.
stain_name
Stain technique
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.
stain_technique
Is batch staining done?
Were the slides stained using a linear batch method or individually?
is_batch_staining_done
Is staining automated?
Was the slide staining automated with an instrument?
is_staining_automated
Preparation instrument vendor
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.
preparation_instrument_vendor
Preparation instrument model
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.
preparation_instrument_model
Slide ID
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
slide_id
Tile configuration
This is how the tiles are configured for stitching.
tile_configuration
Scan direction
This is the direction of imaging, which is required for stitching.
scan_direction
Tiled image columns
This is how many columns used in stitching. This is sometimes referred to as the grid size x.
tiled_image_columns
Tiled image count
This is the total number of raw (tiled) images captured, that are to be stitched together.
tiled_image_count
Intended tile overlap percentage
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.
intended_tile_overlap_percentage
Number of antibodies
number_of_antibodies
Number of channels
The number of distinct color channels in the image.
number_of_channels
Number of biomarker imaging rounds
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.
number_of_biomarker_imaging_rounds
Number of total imaging rounds
The total number of acquisitions performed on microscope to collect autofluorescence/background or stained signal (e.g., histology).
number_of_total_imaging_rounds
Total run time value
How long the tissue was on the acquisition instrument.
total_run_time_value
Total run time unit
The time unit of the total run time.
total_run_time_unit
Organ ID
Unique HuBMAP or SenNet identifier for the organ.
organ_id
Laterality
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.
laterality
Organ condition
Health status of the organ at the time of sample recovery.
organ_condition
Perfusion solution
Type of solution that was used to perfuse the organ.
perfusion_solution
Transport solution
Type of solution used during transport.
transport_solution
Warm ischemic time value
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.
warm_ischemic_time_value
Warm ischemic time unit
The unit of measurement for warm ischemic time.
warm_ischemic_time_unit
Cold ischemic time value
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).
cold_ischemic_time_value
Cold ischemic time unit
The unit of measurement for cold ischemic time.
cold_ischemic_time_unit
Pathology report
General pathologist report. Further details on organ level QC checks.
pathology_report
Weight value
The weight of an entity.
weight_value
Weight unit
The unit of measurement of weight.
weight_unit
Height value
The height of an entity.
height_value
Height unit
The unit of measurement of height.
height_unit
Width value
The width of an entity.
width_value
Width unit
The unit of measurement of width.
width_unit
Length value
The length of an entity.
length_value
Length unit
The unit of measurement of length.
length_unit
Source ID
Unique HuBMAP or SenNet identifier for the source (parent) from which the sample was taken.
source_id
Preparation protocol DOI
The protocol used when procuring or preparing the block, section or suspension. This must be provided as a DOI URL.
preparation_protocol_doi
Parent sample ID
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
parent_sample_id
Library adapter sequence
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).
library_adapter_sequence
Library average fragment size
Average size of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation. Numeric value in base pairs (bp).
library_average_fragment_size
Library input amount value
The amount of cDNA, after amplification, that was used for library construction.
library_input_amount_value
Library input amount unit
Unit of library input amount value.
library_input_amount_unit
Library output amount value
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.
library_output_amount_value
Library output amount unit
Units of library output amount
library_output_amount_unit
Library concentration value
The concentration value of the pooled library samples submitted for sequencing.
library_concentration_value
Library concentration unit
Unit of library concentration value.
library_concentration_unit
Library layout
Whether the library was generated for single-end or paired end sequencing.
library_layout
Number of library PCR cycles
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.
number_of_library_pcr_cycles
Number of PCR cycles for indexing
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.
number_of_pcr_cycles_for_indexing
Library preparation kit
Reagent kit used for library preparation
library_preparation_kit
Sample indexing kit
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).
sample_indexing_kit
Sample indexing set
The specific sequencing barcode index set used, selected from the sample indexing kit.
sample_indexing_set
Is technical replicate?
Is the sequencing reaction run in replicate, "Yes" or "No". If "Yes", FASTQ files in dataset need to be merged.
is_technical_replicate
Expected entity capture count
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.
expected_entity_capture_count
Actual entity input count
Number of cell or nuclei input to the assay. This should be included when available.
actual_entity_input_count
Barcode offset
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.
barcode_offset
Barcode read
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.
barcode_read
Barcode size
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.
barcode_size
UMI offset
Position in the read at which the umi barcode starts. This should be included when constructing sequencing libraries with a non-commercial kit.
umi_offset
UMI read
Which read file contains the UMI barcode. This should be included when constructing sequencing libraries with a non-commercial kit.
umi_read
UMI size
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.
umi_size
Sequencing reagent kit
Reagent kit used for sequencing.
sequencing_reagent_kit
Sequencing read format
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.
sequencing_read_format
Transposition reagent kit
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.
transposition_reagent_kit
Transposition method
Modality of capturing accessible chromatin molecules. For example, this would be the type of kit that was used.
transposition_method
Sequencing batch ID
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.
sequencing_batch_id
Capture batch ID
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.
capture_batch_id
Number of pre-amplification PCR cycles
The number of PCR cycles run after the Chromium controller step and prior to separating the suspension and initiating library construction.
number_of_pre_amplification_pcr_cycles
Assay input unit
Units of assay input amount
assay_input_unit
Assay input entity
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.
assay_input_entity
Number of input cells or nuclei
How many cells or nuclei were input to the assay? This is typically not available for preparations working with bulk tissue.
number_of_input_cells_or_nuclei
Preparation instrument kit
The reagent kit used with the preparation instrument.
preparation_instrument_kit
Amount of input analyte value
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.
amount_of_input_analyte_value
Amount of input analyte unit
Units of amount of entity input to assay value
amount_of_input_analyte_unit
Number of iterations of cDNA amplification
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.
number_of_iterations_of_cdna_amplification
Mapped area value
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.
mapped_area_value
Mapped area unit
The unit of measurement for the mapping area. For Visium and GeoMx this is typically um^2.
mapped_area_unit
Spot size value
Area of a spot in a Visium or HiFi capture area.
spot_size_value
Spot size unit
The unit for spot size value.
spot_size_unit
Number of spots
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.
number_of_spots
Spot spacing value
Approximate center-to-center distance between capture spots. Synonyms: Inter-Spot distance, Spot resolution, Pit size.
spot_spacing_value
Spot spacing unit
Units corresponding to inter-spot distance.
spot_spacing_unit
Capture area ID
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.
capture_area_id
Permeabilization time value
Permeabilization time used for this tissue section.
permeabilization_time_value
Permeabilization time unit
The unit for the permeabilization time.
permeabilization_time_unit
RNA probe panel
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.
rna_probe_panel
Is custom probes used?
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.
is_custom_probes_used
MS ionization technique
The ionization approach (i.e., sample probing method) for performing imaging mass spectrometry.
ms_ionization_technique
Mass analysis polarity
The polarity of the mass analysis (positive or negative ion modes).
mass_analysis_polarity
Mass-to-charge range low value
The low value of the scanned mass-to-charge range, for MS1. (unitless)
mass_to_charge_range_low_value
Mass-to-charge range high value
The high value of the scanned mass-to-charge range, for MS1. (unitless)
mass_to_charge_range_high_value
Mass resolving power
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)
mass_resolving_power
Mass-to-charge resolving power
The peak (m/z) used to calculate the resolving power.
mass_to_charge_resolving_power
Ion mobility
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).
ion_mobility
MS scan mode
MS (mass spectrometry) scan mode refers to the number of steps in the separation of fragments.
ms_scan_mode
Matrix deposition method
Common methods of depositing matrix for assisting in desorption and ionization in imaging mass spectrometry include robotic spotting, electrospray deposition, and sublimation.
matrix_deposition_method
Preparation matrix
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.
preparation_matrix
Desorption solvent
Solvent composition for conducting nanospray desorption electrospray ionization (nanoDESI) or desorption electrospray ionization (DESI).
desorption_solvent
Desorption solvent flow rate value
The rate of flow of the solvent into a spray.
desorption_solvent_flow_rate_value
Desorption solvent flow rate unit
Units of the rate of solvent flow.
desorption_solvent_flow_rate_unit
Analysis protocol DOI
A DOI to a protocols.io protocol describing the software and database(s) used to process the raw data.
analysis_protocol_doi
Data collection mode
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).
data_collection_mode
Label name
If the samples were labeled (e.g. TMT), provide the name/ID of the label on this sample. Leave blank if not applicable.
label_name
LC instrument vendor
The manufacturer of the instrument used for liquid chromatography.
lc_instrument_vendor
LC instrument model
The model number/name of the instrument used for liquid chromatography.
lc_instrument_model
LC column vendor
The manufacturer of the liquid chromatography column unless self-packed, pulled tip capillary is used.
lc_column_vendor
LC column model
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”.
lc_column_model
LC resin
Details of the resin used for liquid chromatography, including vendor, particle size, pore size.
lc_resin
LC column length value
Liquid chromatography column length.
lc_column_length_value
LC column length unit
Units for liquid chromatography column length (typically cm).
lc_column_length_unit
LC temperature value
Liquid chromatography temperature.
lc_temperature_value
LC temperature unit
Units for liquid chromatography temperature.
lc_temperature_unit
LC inner diameter value
Liquid chromatography column inner diameter.
lc_inner_diameter_value
LC inner diameter unit
Units of liquid chromatography column inner diameter (typically microns).
lc_inner_diameter_unit
LC flow rate value
Value of flow rate.
lc_flow_rate_value
LC flow rate unit
Units of flow rate.
lc_flow_rate_unit
LC gradient value
Liquid chromatography gradient.
lc_gradient_value
LC gradient unit
Unit for liquid chromatography gradient.
lc_gradient_unit
LC mobile phase A
Composition of mobile phase A.
lc_mobile_phase_a
LC mobile phase B
Composition of mobile phase B.
lc_mobile_phase_b
Spatial sampling technique
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).
spatial_sampling_technique
Spatial sampling type
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.
spatial_sampling_type
Spatial samping target
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.
spatial_samping_target
Target retrieval incubation temperature
The temperature in Celsius. This will normally be 100 degrees Celsius for RNA assays, and 80 degrees Celsius for protein assays.
target_retrieval_incubation_temperature
Target retrieval incubation time value
The duration for which a sample is exposed to a target retrieval solution.
target_retrieval_incubation_time_value
Target retrieval incubation time unit
The units for target retrieval incubation time value.
target_retrieval_incubation_time_unit
ProteinaseK concentration
The amount or concentration of the enzyme Proteinase K within a sample (in ug/ml).
proteinasek_concentration
ProteinaseK incubation time value
The duration for which a sample is exposed to Proteinase K.
proteinasek_incubation_time_value
ProteinaseK incubation time unit
The units for proteinaseK incubation time value.
proteinasek_incubation_time_unit
Region of interest label
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).
region_of_interest_label
Anatomical structure label
Name of the overarching anatomical structure.
anatomical_structure_label
Anatomical structure ID
The ontology ID for the overarching anatomical structure. Typically this would be an UBERON ID.
anatomical_structure_id
ROI description
A description of the anatomical structure being captured in the region of interest (ROI).
roi_description
ROI ID
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.
roi_id
Acquisition ID
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.
acquisition_id
Area normalized ion dose value
Number of primary ions delivered to the sample per unit area.
area_normalized_ion_dose_value
Area normalized ion dose unit
Area normalized ion dose unit.
area_normalized_ion_dose_unit
Data precision bytes
Numerical data precision in bytes.
data_precision_bytes
Pixel dwell time value
Resident time of primary ion beam on each pixel to ionize it.
pixel_dwell_time_value
Pixel dwell time unit
Pixel dwell time unit.
pixel_dwell_time_unit
Antibodies path
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".
antibodies_path
Ablation frequency unit
Frequency unit of laser ablation.
ablation_frequency_unit
Ablation frequency value
Frequency value of laser ablation.
ablation_frequency_value
Antibody concentration unit
The concentration units of the antibody preparation. Leave blank if not applicable.
antibody_concentration_unit
Channel ID
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.
channel_id
HGNC symbol
Gene symbol approved by HGNC (https://www.genenames.org/) for target gene.
hgnc_symbol
Antibody RRID
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
antibody_rrid
Uniprot accession number
A unique identifier for the target protein in the UniProt database (https://www.uniprot.org).
uniprot_accession_number
Lot number
The lot number is specific to the vendor. Example: Abcam lot number is GR3238979-1
lot_number
Dilution factor
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.
dilution_factor
Antibody concentration value
The concentration value of the antibody preparation. Leave blank if not applicable.
antibody_concentration_value
Conjugated cat number
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.
conjugated_cat_number
Conjugated tag
The name of the entity conjugated to the antibody. Leave blank if not applicable.
conjugated_tag
ROI segmentation strategy
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.
roi_segmentation_strategy
Probe hybridization time unit
The units for probe hybridization time value.
probe_hybridization_time_unit
Oligo probe panel
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.
oligo_probe_panel
Restricted files
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
restricted_files
Cell boundary marker or stain
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.
cell_boundary_marker_or_stain
Nuclear marker or stain
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.
nuclear_marker_or_stain
Parent dataset ID
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
parent_dataset_id
Derived dataset protocol DOI
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.
derived_dataset_protocol_doi
Derived dataset type
The specific type of EPIC analysis being executed.
derived_dataset_type
Primary dataset type
The type of primary dataset used to derive this EPIC.
primary_dataset_type
Number of files containing masks
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.
number_of_files_containing_masks
Number of masks
How many masks are included, inclusive of all OME TIFF files.
number_of_masks
Target name
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.
target_name
Isotype
Describes the antibody isotype. Please write out any symbols. (e.g. IgG, IgG1, IgG1 kappa)
isotype
Host
This is the species that was used to generate the antibody (e.g. mouse, rabbit, etc).
host
Clonality
This will be either Monoclonal or Polyclonal.If monoclonal provide the clone ID or identify the antibody as polyclonal.
clonality
Antibody vendor
This is the company that sells the antibody.
antibody_vendor
Catalog number
Provides catalog number from vendor for the source of the antibody.
catalog_number
Recombinant
Simple Yes or No if the antibody was recombinant. Recombinant antibodies (rAbs) are monoclonal antibodies which are generated in vitro using synthetic genes.
recombinant
Assay method
This is the downstream assay that was used (e.g. CODEX, MIBI, etc).
assay_method
Tissue preservation technique
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).
tissue_preservation_technique
Author ORCID
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/
author_orcid
Vendor affiliation
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)
vendor_affiliation
Organ name
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.
organ_name
Antigen retrieval
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.
antigen_retrieval
AVR filename
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.
avr_filename
OMAP ID
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)
omap_id
Cycle number
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).
cycle_number
Fluorescent reporter
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).
fluorescent_reporter
Is channel used for nuclei segmentation?
Specifies if this channel can be used by algorithms performing nuclei segmentation ("Yes" or "No").
is_channel_used_for_nuclei_segmentation
Is channel used for cell segmentation?
Specifies if this channel can be used by algorithms performing cell segmentation ("Yes" or "No").
is_channel_used_for_cell_segmentation
Is antibody
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.
is_antibody
Antibody reagent kit
antibody_reagent_kit
Viability reagent kit
viability_reagent_kit
Instrument calibration bead kit
instrument_calibration_bead_kit
Loaded cell concentration unit
loaded_cell_concentration_unit
Chemistry kit
chemistry_kit
Pixel physical size height unit
pixel_physical_size_height_unit
Pixel physical size width unit
pixel_physical_size_width_unit
Pixel physical size depth unit
pixel_physical_size_depth_unit
Capture area width unit
capture_area_width_unit
Capture area height unit
capture_area_height_unit
Spatial discretization method
spatial_discretization_method
Signal quenching method
signal_quenching_method
Magnetic resonance
An acquisition device, process or method that performs magnetic resonance imaging.
Magnetic Resonance
Aspen chip bedding
Organism housed with bedding made from all natural aspen chips.
Aspen shaving bedding
Organism housed with bedding made from all natural aspen shavings.
Corn cob bedding
Organism housed with bedding made from ground corn cobs.
Pine chip bedding
Organism housed with bedding made from all natural pine chips.
Pine shaving bedding
Organism housed with bedding made from all natural pine shavings.
Laser ablation
Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by light amplification by stimulated emission of radiation.
Healthy
Having no significant health-related issues.
Cell
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
Created, done, or existing within a company or organization.
In-House
Nucleus
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
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
Refers to a process where a sample is preserved with formalin and then embedded into a paraffin block for sectioning.
FFPE (Paraffin embedded)
Thermal Ionization Mass Spectrometry
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.
TIMS
Data-Dependent Acquisition
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.
DDA
Data-Independent Acquisition
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
DIA
Selected Reaction Monitoring
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.
SRM
Parallel Reaction Monitoring
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.
PRM
Collagen
A family of large fibrous proteins that are the main components of connective tissue and are responsible for maintaining tissue structure.
Protein
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
The read direction identified as number 1 in a paired-end nucleotide sequencing reaction.
Read 1 (R1)
Read pair 2
The read direction identified as number 2 in a paired-end nucleotide sequencing reaction.
Read 2 (R2)
Diseased
An indication that an anatomic structure has detectable aberrations.
NP40 Lysis Buffer
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.
Lysis buffer
Roswell Park Memorial Institute 1640 Medium
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]
RPMI
Unknown
Not known, observed, recorded; or reported as unknown by the data contributor.
PAXgene tissue system
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.
PAXgene tissue kit (PXT)
Liquid nitrogen storage
An indication that a material has been stored in liquid nitrogen.
Frozen in liquid nitrogen
Liquid nitrogen vapor storage
An indication that a material has been stored in liquid nitrogen vapor.
Frozen in liquid nitrogen vapor
Dulbecco's Modified Eagle Medium
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]
DMEM
Frozen on dry ice
A sample that is in a frozen state maintained with dry ice.
Laser Capture Microdissection
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.
LCM
Electrospray ionization
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)
ESI
Cell segmentation
The computational process of identifying and separating individual cells within an image.
Right
Being or located on or directed toward the side of the body to the east when facing north.
Left
Being or located on or directed toward the side of the body to the west when facing north.
cDNA
Single-stranded DNA that is complementary to messenger RNA or DNA that has been synthesized from messenger RNA by reverse transcriptase.
None
No person or thing, nobody, not any.
Hertz
A SI derived unit of frequency; equal to one oscillation (one cycle) per second.
DNA
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
Determination of a value is not relevant in the current context.
Metabolite
Any substance involved in metabolism, either as a product of metabolism or as necessary for metabolism.
Lipid
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
Trade name for an aqueous, non-toxic tissue storage reagent that rapidly permeates tissues to stabilize and protect cellular RNA.
RNAlater
Optimal cutting temperature compound
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.
OCT
Water
H2O, a clear, colorless, odorless, tasteless liquid that freezes into ice below 0 degrees centigrade and boils above 100 degrees centigrade.
Customize
To make according to individual requirements or specifications; to make more personalized or tailored for a specific need.
Custom
Gelatin
Kilohertz
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.
kHz
Megahertz
The SI derived unit of frequency; equal to one million oscillations per second or to 10E6 hertz.
MHz
Specimen at room temperature
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).
Stored in ambient temperature
Peptide
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
A medial line, especially the medial line or medial plane of the body (or some part of the body).
RNA
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
CMC
Formic acid
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.
Formic acid in water
Male
Orgamism is male.
Female
Orgamism is female.
Standard/default
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
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]
AB-PAS
Hematoxylin and eosin stain
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.
H&E
Luxol fast blue/Cresyl violet stain
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.
LFB
Periodic acid-Schiff stain
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.
PAS
Sudan black B stain
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]
SBB
Trichrome stain
Acid dyes and washes to selectively dye the structural elements in tissue samples in three or more contrasting colors.
Trichrome
Other
Organism housed in a room with alternative health status not specified.
Organism housed in cages not specified.
Organism housed with bedding not specified.
Organism housed with light cycle not specified.
Organism housed with nesting/chewing implements not specified.
Organism was euthanized via alternative method not specified.
Periodate-lysine-paraformaldehyde
Combination of periodate, lysine and paraformaldehyde; used as a fixative for the study of duodenal mucosa.
PLP (Periodate-Lysine-Paraformaldehyde)
4-(dimethylamino)cinnamic acid
DMACA (4-(dimethylamino)cinnamic acid)
Photobleaching
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
A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group.
2,5-Dihydroxybenzoic acid
A dihydroxybenzoic acid having the two hydroxy groups at the 2- and 5-positions.
2,5-DHB (2,5-Dihydroxybenzoic acid)
2',5'-Dihydroxyacetophenone
2,5-DHA (2,5-dihydroxyacetophenone)
Methanol
The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group.
Polysaccharide
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
A fluorescent dye used to stain biological specimens.
N-(1-naphthyl)ethylenediamine dihydrochloride
An ethylenediamine dihydrochloride compound having an N-(1-naphthyl) substituent.
NEDC (N-(1-naphthyl) ethylenediamine dihydrochloride)
Paraformaldehyde polymer
A poly(oxymethylene) polymer, composed of paraformaldehyde macromolecules.
PFA (Paraformaldehyde)
alpha-cyano-4-hydroxycinnamic acid
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.
CHCA (alpha-cyano-4-hydroxy-cinnamic acid)
9-aminoacridine
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.
9-AA (9-aminoacridine)
sinapic acid
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.
SA (sinapic acid)
Matrix-assisted laser desorption ionization
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.
MALDI
Laser desorption ionization
The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material.
LDI
Desorption electrospray ionization
Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure.
DESI
Neutral buffered formalin
A processed material that is a mixture of formalin (formaldehyde), phosphates, and water used as a standard fixative for diagnostic preparations.
NBF (Neutral Buffered Formalin)
Enzymatic cleavage
A material processing that digests the fraction of input material that is susceptible to that enzyme
paired-end library
is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
paired-end
single-end library
A cDNA library that is a collection of short tags from only one end of DNA fragments.
single-end
Single-cell ATAC-seq
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.
scATACseq
Bulk assay for transposase-accessible chromatin using sequencing
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.
bulkATACseq
Nanospray desorption electrospray ionization assay
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.
nanoDESI
Nanodroplet Processing in One pot for Trace Samples
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.
nanoPOTS
Single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing
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.
sciATACseq
Phosphate buffered saline solution
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).
PBS
Decapitation
Organism was euthanized by physical removal of head from the body
Intravenous anesthetic euthanasia
Organism was euthanized by intravenous injection of anesthetic.
Cervical dislocation
Organism was euthanized by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion.
Carbon dioxide inhalant euthanasia
Organism was euthanized by inhalation of carbon dioxide.
kilogram
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
centimeter
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
millimeter
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
micrometer
A length unit which is equal to one millionth of a meter or 10^[-6] m.
nanometer
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
gram
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
milligram
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
microgram
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
nanogram
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
degree Celsius
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.
celsius
millisecond
A time unit which is equal to one thousandth of a second or 10^[-3] s.
minute
A time unit which is equal to 60 seconds.
hour
A time unit which is equal to 3600 seconds or 60 minutes.
day
A time unit which is equal to 24 hours.
month
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
A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days.
nanomolar
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
square millimeter
An area unit which is equal to one millionth of a square meter or 10^[-6] m^[2].
mm^2
cubic centimeter
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
cm^3
milliliter
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
microliter
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
hertz
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
microliters per minute
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
uL/min
microgram per milliliter
A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters.
ug/ml
square micrometer
An area unit which is equal to an area enclosed by a square with sides each 1 micrometer long.
um^2
nanogram per microliter
A mass unit density which is equal to mass of an object in nanograms divided by the volume in microliters.
ng/ul
monoclonal
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.
Monoclonal
polyclonal
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.
Polyclonal
Thermo Fisher Scientific
Commercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.
Leica Microsystems
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
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.
Millipore
Miltenyi Biotec
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
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
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
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.
NextSeq 500
Illumina NextSeq 550 System
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.
NextSeq 550
Illumina HiSeq 2500 System
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.
HiSeq 2500
Illumina HiSeq 3000/HiSeq 4000 System
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.
HiSeq 4000
Illumina NovaSeq 6000 System
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.
NovaSeq 6000
Hamamatsu Photonics
Manufacturer of optical sensors including, photomultiplier tubes, electric light sources, and other optical devices and their applied instruments for scientific, technical and medical use.
Hamamatsu
Keyence BZ-X710 fluorescent microscope
All in one fluorescence microscope BZ-X710 by Keyence, Japan.
BZ-X710
Bruker Corporation
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.
Bruker
Zeiss LSM 710 Confocal Inverted Microscope
Inverted microscope that enables confocal microscopy in cell and developmental biology.
LSM 710 Confocal Microscope
10x Genomics Chromium Plus Genetic Analyzer
Genetic analyzer, referred to as Chromium Controller for combining large partition numbers with a diverse barcode library to generate >100,000 barcode-containing partitions.
Chromium Controller
Fluidigm CyTOF Helios mass cytometer
Mass cytometer that enables deep profiling of translational and clinical research samples across range of cell surface and intracellular markers.
Helios
Sciex QTRAP 5500 mass spectrometer
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.
QTRAP 5500
Thermo Scientific Q Exactive HF Hybrid Quadrupole-Orbitrap mass spectrometer
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.
Q Exactive HF
Thermo Scientific Orbitrap Fusion Tribrid mass spectrometer
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.
Orbitrap Fusion Tribrid
Thermo Scientific Orbitrap Fusion Lumos Tribrid mass spectrometer
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.
Orbitrap Fusion Lumos Tribrid
Thermo Scientific Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass Spectrometer
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.
Q Exactive HF-X
Thermo Scientific Q Exactive GC Orbitrap mass spectrometry
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.
Q Exactive
Thermo Scientific Q Exactive UHMR Hybrid Quadrupole-Orbitrap Mass Spectrometer
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.
Q Exactive UHMR
Zeiss Lightsheet Z.1 fluorescence microscope
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.
Zeiss LightSheet Z.1
Zeiss Axio Scan.Z1 Slide Scanner
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.
Axio Scan.Z1
Leica Aperio AT2 Scanner
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.
Aperio AT2
Hamamatsu NanoZoomer 2.0-HT Digital slide scanner
High speed, high resolution digital scanner with network features. User friendly full slide scanner designed to process up to 210 slides automatically.
NanoZoomer 2.0-HT
NanoString GeoMx Digital Spatial Profiler
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.
Digital Spatial Profiler
Biomark HD system
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.
Biomark HD
Hyperion Imaging System
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
Brightfield and fluorescent whole slide imager with Multispectral Imaging Technology.
Cytiva
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
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
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
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
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.
Standard BioTools (Fluidigm)
Zeiss Microscopy
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
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
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.
Zyla 4.2 sCMOS
Leica SCN400 slide scanner
Provides fully digitized image of speciment that can be viewed and edited from virtually anywhere.
SCN400
Ionpath MIBIscope System
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.
MIBIscope
Illumina NextSeq 2000 System
Sequencing system supports range of methods such as exome sequencing, target enrichment, single-cell profiling.
NextSeq 2000
Bruker timsTOF fleX with MALDI-2
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.
timsTOF FleX MALDI-2
GE Healthcare IN Cell Analyzer 2200
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.
IN Cell Analyzer 2200
Keyence BZ-X800 fluorescent microscope
Automated high-resolution microscope for Life Science research.
BZ-X800
Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer
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.
Orbitrap Eclipse Tribrid
Sciex
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
American biotechnology company that designs and manufactures gene sequencing technology used in scientific research.
Zeiss Axio Observer 5
Inverted microscope Axio Observer 5 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging.
Axio Observer 5
Zeiss Axio Observer 3
Inverted microscope Axio Observer 3 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging.
Axio Observer 3
Zeiss Axio Observer 7
Inverted microscope Axio Observer 7 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging.
Axio Observer 7
HTX Sublimator
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.
Sublimator
HTX M3+ Sprayer
Sample preparation platform offering automated advanced MALDI matrix sprayer.
M3+ Sprayer
HTX TM-Sprayer
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.
TM-Sprayer
HTX M5 Sprayer
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.
M5 Sprayer
HTX Technologies
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
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.
NanoZoomer S210
Hamamatsu NanoZoomer S360 Digital slide scanner
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.
NanoZoomer S360
Hamamatsu NanoZoomer S60 Digital slide scanner
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.
NanoZoomer S60
Hamamatsu NanoZoomer-SQ Digital slide scanner
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.
NanoZoomer-SQ
Phenocycler-Fusion
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.
Phenocycler-Fusion 2.0
Akoya Biosciences
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
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.
SunCollect Sprayer
SunChrom
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
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.
CosMx Spatial Molecular Imager
10x Genomics Xenium Analyzer
Xenium Analyzer offers subcellular profiling of 100s to 1,000s of RNA targets alongside multiplexed protein, in fresh, frozen or FFPE tissue.
Xenium Analyzer
Resolve Biosciences
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
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.
NanoString
Leica Autostainer ST5010 XL
Leica ST5010 Autostainer XL provides reproducible, consistent high quality staining, and increased workload throughput compared to manual staining.
AutoStainer XL
Zeiss Lightsheet 7
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.
Lightsheet 7
Resolve Biosciences Molecular Cartography
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
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.
Chromium iX
10x Genomics Chromium X Single Cell Analyzer
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.
Chromium X
Illumina NovaSeq X Plus
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.
NovaSeq X Plus
Illumina NovaSeq X
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.
NovaSeq X
Visium CytAssist
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
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
Business Services and Biotechnology Research company in Odense, Denmark.
IonOpticks
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
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.
STELLARIS 5
Evident
Company for development, manufacture, sale and provision of solutions for biological microscopes, industrial microscopes, industrial endoscopes, non-destructive inspection equipment, X-ray analyzers, etc.
Evident Scientific (Olympus)
Olympus VS200 Slide Scanner
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.
VS200 Slide Scanner
3DHISTECH Pannoramic MIDI II Scanner
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.
Pannoramic MIDI II Digital Scanner
MGI DNBSEQ-T7 Genetic Sequencer
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.
DNBSEQ-T7
BGI Genomics
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
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
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
Leica DM6 B Upright Microscope includes the Leica DFC7000 T Camera and LAS X Software.
DM6 B
TissueScope LE Slide Scanner
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
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
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.
ST5020 Multistainer
EVOS M7000 Imaging System
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.
EVOS M7000
Roche Diagnostics
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
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.
Discovery Ultra
Leica Aperio CS2 Scanner
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.
Aperio CS2
10x Genomics Chromium Connect system
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.
Chromium Connect
Keyence BZ-X810 microscope
Inverted fluorescence phase contrast microscope. Objective lenses. BZ Series infinite optical system.
BZ-X810
Discovery MR750 3.0T MR system
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.
Discovery MR750
GE HealthCare
Provides digital infrastructure, data analytics and decision support tools to help in diagnosis, treatment and monitoring of patients.
GE Healthcare
Shimadzu
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
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.
MERSCOPE Ultra
Vizgen
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
Fully automated and affordable cytometer to simplify and standardize deep single-cell profiling studies.
CyTOF XT
Element AVITI24 system
Element AVITI24 system is the benchtop platform enabling high-quality, low-cost sequencing and single cell multiomics in one powerful system.
AVITI
Element Biosciences
Biotechnology company in San Diego, California focused on developing disruptive DNA sequencing and other omics technology for research markets.
Bruker timsTOF Ultra mass spectrometer
Mass spectrometer used for proteomics research. Offers the ultimate fusion of trapped ion mobility spectrometry (TIMS) with quadrupole time-of-flight (QTOF) technology.
timsTOF Ultra
Bruker timsTOF Ultra 2 mass spectrometer
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.
timsTOF Ultra 2
Bruker timsTOF SCP mass spectrometer
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.
timsTOF SCP
Bruker timsTOF HT mass spectrometer
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.
timsTOF HT
Bruker timsTOF Pro mass spectrometer
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.
timsTOF Pro
Bruker timsTOF Pro 2 mass spectrometer
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.
timsTOF Pro 2
Fluidigm CyTOF 2 mass cytometer
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.
CyTOF 2
Leica DMi8 Inverted Microscope
Leica DMi8 microscope is an inverted light microscope, intended as a general microscope for routine examinations of biological specimens.
DMi8
Singular Genomics
Publicly-traded life science technology company, which specializes in advanced next-generation sequencing (NGS) and multiomic technologies.
Singular Genomics G4X Spatial Sequencer
Ultra high-throughput, spatial sequencing platform, for integrated multiomic analysis of FFPE samples at subcellular resolution. Spatial sequencing platform capable of simultaneous direct RNA.
G4X Spatial Sequencer
Bruker timsTOF FleX
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.
timsTOF FleX
Complete Genomics
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
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
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
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.
Cytek Northern Lights
Zeiss Axio Zoom.V16 for Biology
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.
Axio Zoom.V16
Microscopes International
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
Bruker solariX is magnetic resonance mass spectrometry (MRMS) platform, available with high-field magnets ranging from 7 T up to 15 T.
solariX
Microscopes International uScopeHXII-20 microscope
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.
uScopeHXII-20
Fluidigm Juno Targeted DNA Sequencing Library Preparation System
Juno system used for preparing libraries for next-generation sequencing and IFS preparation for gene expression, genotyping and digital PCR application.
Juno System
Leica Cell DIVE Multiplex Imaging Solution System
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.
Cell DIVE
3DHISTECH Pannoramic 150 Digital Scanner
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.
Panoramic 150 Digital Scanner
Revvity Inc.
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.
Revvity
Revvity Opera Phenix Plus High Content Screening system
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.
Opera Phenix Plus HCS
Waters SYNAPT G2-Si mass spectrometry system
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.
SYNAPT G2-Si
PerkinElmer Opera Phenix High Content Screening System
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.
Opera Phenix HCS
Miltenyi Biotec MACSima System
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.
MACSima System
Hamamatsu NanoZoomer 2.0-RS Digital slide scanner
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).
NanoZoomer 2.0-RS
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]
Regressive staining
Stored in refrigerator
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
Inflated (Agarose)
Frozen at -20 degrees celsius
Left-and-down
Snake-by-columns
Left-and-up
um^3
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]
Modified progressive staining
DMSO (no serum)
Fixed frozen OCT (Formalin, sucrose protected)
Allprotect tissue reagent (ALL)
Snake-by-rows
Inflated (OCT)
DMSO (serum)
Fresh frozen OCT
Fresh frozen CMC
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]
Endogenous fluorophore
Frozen at -80 degrees celsius
Column-by-column
CLARITY hydrogel
Tris-EDTA
mm^3
Right-and-down
Row-by-row
Bouin's
Right-and-up
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]
Progressive staining
A sample that is in a frozen state maintained with ice.
Frozen on ice
Fixed frozen OCT (PFA, sucrose protected)
Incubated at 37 degrees celsius
Fixed frozen OCT (Cytofix/Cytoperm)
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]
Miltenyi Tissue Preservation Buffer
University of Wisconsin Solution
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]
UW Solution
UWS Solution
Histidine-Tryptophan-Ketoglutarate Solution
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]
HTK Solution
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]
Belzer MPS/KPS
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]
Saline (Buffered)
Cell DIVE dataset
Dataset generated from performing the Cell DIVE assay.
CODEX dataset
Dataset generated from performing the CODEX assay.
CODEX
Light Sheet dataset
Dataset generated from performing the Light Sheet assay.
Light Sheet
MIBI dataset
Dataset generated from performing the Multiplex Ion Beam Imaging (MIBI) assay.
MIBI
snATACseq dataset
Dataset generated from performing the snATAC-seq assay.
snATACseq
snRNAseq dataset
Dataset generated from performing the snRNA-seq assay.
snRNAseq
Visium dataset
Dataset generated from performing the Visium assay.
Visium
LC-MS dataset
Dataset generated from performing the LC-MS assay.
LC-MS
HiFi-Slide dataset
Dataset generated from performing the HiFi-Slide assay.
HiFi-Slide
Histology dataset
Dataset generated from performing the Histology assay.
Histology
Fresh frozen gelatin
PhenoCycler dataset
Dataset generated from performing the PhenoCycler assay.
PhenoCycler
CyCIF dataset
Dataset generated from performing the CyCIF assay.
CyCIF
MALDI dataset
Dataset generated from performing the MALDI assay.
SIMS dataset
Dataset generated from performing the SIMS assay.
SIMS
DESI dataset
Dataset generated from performing the DESI assay.
Auto-fluorescence dataset
Dataset generated from performing the Auto-fluorescence assay.
Auto-fluorescence
Confocal dataset
Dataset generated from performing the Confocal assay.
Confocal
Thick section Multiphoton MxIF dataset
Dataset generated from performing the Thick section Multiphoton MxIF assay.
Thick section Multiphoton MxIF
Second Harmonic Generation (SHG) dataset
Dataset generated from performing the Second Harmonic Generation assay.
Second Harmonic Generation (SHG)
Enhanced Stimulated Raman Spectroscopy (SRS) dataset
Dataset generated from performing the Enhanced Stimulated Raman Spectroscopy assay.
Enhanced Stimulated Raman Spectroscopy (SRS)
ATACseq (bulk) dataset
Dataset generated from performing the Bulk ATACseq assay.
ATACseq (bulk)
RNAseq (bulk) dataset
Dataset generated from performing the Bulk RNAseq assay.
RNAseq (bulk)
10X Multiome dataset
Dataset generated from performing the 10X Multiome assay.
10X Multiome
Molecular Cartography dataset
Dataset generated from performing the Molecular Cartography assay.
Molecular Cartography
CosMx Transcriptomics dataset
Dataset generated from performing the CosMx Transcriptomics assay.
CosMx Transcriptomics
Xenium dataset
Dataset generated from performing the Xenium assay.
Xenium
MERFISH dataset
Dataset generated from performing the MERFISH assay.
MERFISH
Travelling Wave Ion Mobility Spectrometry
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]
TWIMS
Field Asymmetric Ion Mobility Spectrometry
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]
FAIMS
Dispersive or Drift Tube Ion Mobility Spectrometry
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]
DTIMS
Structures for Lossless Ion Manipulations
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]
SLIM
Cyclic Ion Mobility Spectrometry
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]
cIMS
MS1
MS2
MS3
A desolvent mixture created by mixing methanol (MeOH) and water (H2O). [Generated by an AI language model]
Methanol:Water (MeOH:H2O)
A desolvent mixture created by mixing methanol (MeOH) and ethanol (EtOH). [Generated by an AI language model]
Methanol:Ethanol (MeOH:EtOH)
A desolvent mixture created by mixing acetonitrile (ACN) and water (H2O). [Generated by an AI language model]
Acetonitrile:Water (ACN:H2O)
A desolvent mixture created by mixing acetonitrile (ACN) and dimethylformamide (DMF). [Generated by an AI language model]
Acetonitrile:Dimethylformamide (ACN:DMF)
A desolvent mixture created by mixing ethanol (EtOH) and water (H2O). [Generated by an AI language model]
Ethanol:Water (EtOH:H2O)
A desolvent mixture created by mixing ethanol (EtOH) and dimethylformamide (DMF). [Generated by an AI language model]
Ethanol:Dimethylformamide (EtOH:DMF)
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]
Robotic spotting
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]
Electrospray deposition
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]
Robotic spraying
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]
Sublimation
DAN (1,5-diaminonapthalene)
scATACseq dataset
Dataset generated from performing the scATAC-seq assay.
scRNAseq dataset
Dataset generated from performing the scRNA-seq assay.
scRNAseq
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]
Perfadex Plus
10x Genomics; Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns; PN 1000283
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]
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
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]
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
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]
10X Genomics; Single Index Kit N, Set A (96 rxn); PN 1000212
10x Genomics; Dual Index Kit TT, Set A, 96 rxns; PN 1000215
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]
10X Genomics; Dual Index Kit TT, Set A (96 rxn); PN 1000215
Illumina; HiSeq 3000/4000 PE Cluster Kit PE-410-1001; PN 1000283
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
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]
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
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
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
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
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
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]
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
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]
10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 reactions; PN 1000184
SNARE-seq2 dataset
Dataset generated from performing the SNARE-seq2 assay.
SNARE-seq2
10x Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 1 slides, 4 rxns; PN 1000187
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]
10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 1 slides, 4 reactions; PN 1000187
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]
tissue (bulk)
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 cell
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]
single nucleus
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]
spot
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]
area of interest
Nucleic acid + protein
10x Genomics; Visium Human Transcriptome Probe Kit v2 - Small; PN 1000466
nL/min
Negative ion mode
Positive ion mode
Negative and positive ion mode
MALDI-2
SIMS-C60
SIMS-H20
10x Genomics; Dual Index Kit TS, Set A; PN 1000251
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]
10X Genomics; Dual Index Kit TS, Set A; PN 1000251
Illumina; NovaSeq X Series 10B Reagent Kit (300 Cycle); PN 20085594
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
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
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
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
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
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
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]
HESI
mL/min
Liquid Extraction Surface Analysis
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]
LESA
Microscale Liquid Extraction Surface Analysis
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]
microLESA
Microscale Pots for Analysis of Transferred Samples
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]
microPOTS
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]
Profiling
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]
Imaging
2D Imaging Mass Cytometry dataset
Dataset generated from performing the 2D Imaging Mass Cytometry assay.
2D Imaging Mass Cytometry
nanoSPLITS
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]
nA*hr/mm2
10x Genomics; Chromium Single Cell 3' Library & Gel Bead Kit, 4 rxns; PN 120267
10X Genomics; Chromium Single Cell 3' Library & Gel Bead Kit, 4 rxns; PN 120267
GeoMx (NGS) dataset
Dataset generated from performing the GeoMx (NGS) assay.
GeoMx (NGS)
GeoMx (nCounter) dataset
Dataset generated from performing the GeoMX (nCounter) assay.
GeoMx (nCounter)
Visium (no probes) dataset
Dataset generated from performing the Visium (no probes) assay.
Visium (no probes)
Visium (with probes) dataset
Dataset generated from performing the Visium (with probes) assay.
Visium (with probes)
Automated segmentation
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
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
10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome 4 rxns x 4 BC; PN 1000475
ATACseq dataset
Dataset generated from performing the ATACseq assay.
ATACseq
RNAseq dataset
Dataset generated from performing the RNAseq assay.
RNAseq
RNAseq (with probes) dataset
Dataset generated from performing the RNAseq (with probes) assay.
RNAseq (with probes)
nanoSPLITS dataset
Dataset generated from performing the nanoSPLITS assay.
Illumina; NovaSeq 6000 S1 Reagent Kit (200 Cycles); PN 20012864
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
Dataset generated from performing segmentation mask pipeline.
Segmentation Mask
Phenocycler-Fusion 1.0
Custom: Multiphoton
Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (300 Cycles); PN 20028317
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
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
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
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
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
10x Genomics; Visium FFPE Reagent Kit v2-Small; PN 1000436
10X Genomics; Visium FFPE Reagent Kit v2-Small, PN 1000436
10x Genomics; Chromium Next GEM Chip Q Single Cell Kit, 16 rxns; PN 1000422
10X Genomics; Chromium Next GEM Chip Q Single Cell Kit, 16 rxns; PN 1000422
10x Genomics; Visium Human Transcriptome Probe Kit-Small; PN 1000363
DNA + RNA
MUSIC
Dataset generated from performing the MUSIC assay.
Hematoxylin and 3,3′-Diaminobenzidine stain
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]
H-DAB
Biops buffer
Trumps fixative
2% PFA/2.5% Glutaraldehyde
Cryo-EM
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' 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
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
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
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
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
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
10X Genomics; Chromium Next GEM Single Cell 5' Kit v2, 4 rxns; PN 1000265
Parse Biosciences; Evercode WT v2 Kit, 48 rxns; PN ECW02030
Parse Biosciences; Evercode WT Mini v2 Kit, 12 rxns; PN ECW02010
Illumina; TruSeq Stranded mRNA Library Prep (48 samples); PN 20020594
Illumina; TruSeq Stranded mRNA Library Prep (96 samples); PN 20020595
Parse Biosciences; Fragmentation Reagents; PN WX100
Parse Biosciences; UDI Plate - WT; PN UDI1001
Illumina; TruSeq RNA Single Indexes Set A (12 Indexes, 48 Samples); PN 20020492
Illumina; TruSeq RNA Single Indexes Set B (12 Indexes, 48 Samples); PN 20020493
Illumina; TruSeq RNA CD Index Plate (96 Indexes, 96 Samples); PN 20019792
Illumina; IDT for Illumina - TruSeq RNA UD Indexes v2 (96 Indexes, 96 Samples); PN 20040871
Integrated DNA Technologies: Custom DNA Oligos
Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (200 Cycles); PN 20046812
Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (300 Cycles); PN 20046813
Illumina; NextSeq 2000 P3 Reagent Kit (300 Cycles); PN 20040561
10x Genomics; Visium Spatial for FFPE Gene Expression Kit, Mouse Transcriptome, 4 rxns; PN 1000339
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
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
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
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
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
Illumina; NextSeq 2000 P3 Reagents Kit (100 Cycles); PN 20040559
10x Genomics; Visium Mouse Transcriptome Probe Kit - Small; PN 1000365
NanoString Technologies; GeoMx Human Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-HuWTA-4
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
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
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
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
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
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
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]
Illumina; NextSeq 500/550 Mid Output Kit 150 Cycles v2.5; PN 20024904
Modified Davidson's Fixative
Alpha-MEM
Growth media
10x Genomics; Chromium Next GEM Chip K Automated Single Cell Kit, 48 rxns; PN 1000289
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
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
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
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
10x Genomics; Chromium Next GEM Chip G Single Cell Kit, 48 rxns; PN 1000120
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
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
10X Genomics; Chromium i7 Sample Index Plate (96 rxn); PN 220103
Illumina; NextSeq 500/550 Hi Output v2.5 Kit (75 Cycles); PN 20024906
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
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
Resolve
Dataset generated from performing the Resolve assay.
Stereo-seq
Dataset generated from performing the Stereo-seq assay.
Hydroxypropyl Methylcellulose-Polyvinylpyrrolidone
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]
HPMC-PVP
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]
Stored in desiccator
Saturated lipid
Unsaturated lipid
Seq-Scope dataset
Dataset generated from performing the Seq-Scope assay.
Seq-Scope
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]
Concentrated quench buffer
Illumina; NovaSeq X Series 25B Reagent Kit (300 Cycle); PN 20104706
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
10x Genomics; Chromium GEM-X Single Cell 5' Kit v3, 16 rxns; PN 1000699
10x Genomics; Xenium Human Multi-Tissue and Cancer Panel v1; PN 1000626
DART-FISH
Dataset generated from performing the DART-FISH assay.
seqFISH
Dataset generated from performing the seqFISH assay.
10x Genomics; Library Construction Kit C, 4 rxns; PN 1000689
10x Genomics; Library Construction Kit C, 16 rxns; PN 1000694
10x Genomics; Chromium GEM-X Single Cell 3' Kit v4, 16 rxns; PN 1000691
Lipid + metabolite
Object x Analyte dataset
Object x Analyte
MERSCOPE
MS Lipidomics
Dataset generated from performing the MS Lipidomics assay.
Element Biosciences; AVITI 2x75 Sequencing Kit Cloudbreak FS High Output (184 Cycles); PN 860-00015
CyTOF
Dataset generated from performing the CyTOF assay.
Standard BioTools; Maxpar Phosphoprotein Staining Kit; PN 201604
Standard BioTools; Maxpar Nuclear Antigen Staining Kit; PN 201603
Standard BioTools; Maxpar Cytoplasmic/Secreted Antigen Staining Kit; PN 201602
Standard BioTools; Maxpar Cell Surface Staining Kit; PN 201601
Standard BioTools; Cell-ID Cisplatin 100 uL; PN 201064
Standard BioTools; Cell-ID Cisplatin-194Pt 100 uL; PN 201194
Standard BioTools; Cell-ID Cisplatin-195Pt 100 uL; PN 201195
Standard BioTools; Cell-ID Cisplatin-196Pt 100 uL; PN 201196
Standard BioTools; Cell-ID Cisplatin-198Pt 100 uL; PN 201198
Standard BioTools; Cell-ID Intercalator-103Rh 500 um; PN 201103A
Standard BioTools; Cell-ID Intercalator-103Rh 2,000 um; PN 201103B
Sigma Aldrich; Cisplatin 25mg; PN P4394
Standard BioTools; CyTOF Calibration Beads; PN 201073
Standard BioTools; EQ Four Element Calibration Beads 100 mL; PN 201078
Standard BioTools; EQ Six Element Calibration Beads 100 mL; PN 201245
cells/mL
Nucleus + cell
1X fixation & permeabilization buffer
10x Genomics; Xenium Prime 5K Human Pan Tissue & Pathways Panel; PN 1000724
1X quench buffer
DBiT-seq dataset
Dataset generated from performing the DBiT-seq assay.
DBiT-seq
Singular Genomics G4X dataset
Dataset generated from performing the Singular Genomics G4X assay.
Singular Genomics G4X
NanoString Technologies; CosMx Human Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-H-USCP-1KP-R
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
10x Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Mouse Transcriptome, 6.5mm, 4 rxns; PN 1000521
A prototype of MALDI timsTOF FleX
MALDI timsTOF Flex Prototype
CosMx Proteomics dataset
Dataset generated from performing the CosMx Proteomics assay.
CosMx Proteomics
NanoString Technologies; CosMx Human Immuno-Oncology Panel (Protein, 64 Plex); PN CMX-H-IOP-64P-P
NanoString Technologies; CosMx Mouse Neuroscience Panel (Protein, 64 Plex); PN CMX-M-Neuro-64P-P
picogram per microliter
A mass unit density which is equal to mass of an object in picograms divided by the volume in microliters.
pg/ul
10x Genomics; Library Construction Kit, 16 rxns; PN 1000190
FACS dataset
Dataset generated from performing the Fluorescence-Activated Cell Sorting (FACS) assay.
FACS
Olink dataset
Dataset generated from performing the Olink assay.
Olink
10x Genomics; Xenium Mouse Multi-Tissue Atlassing Panel; PN 1000627
10x Genomics; Xenium Human Lung Gene Expression Panel; PN 1000601
10x Genomics; Xenium Custom Gene Expression Panel, (51-100 genes); PN 1000561
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
10x Genomics; Xenium Human Colon Gene Expression Panel; PN 1000642
4i dataset
Dataset generated from performing the 4i assay.
MPLEx dataset
Dataset generated from performing the MPLEx assay.
MPLEx
Pixel-seqV2 dataset
Dataset generated from performing the Pixel-seqV2 assay.
Pixel-seqV2
Visium HD dataset
Dataset generated from performing the Visium HD assay.
Visium HD
NanoString Technologies; CosMx Mouse Neuroscience Panel (RNA, 1000 Plex); PN CMX-M-NEUP-R
NanoString Technologies; CosMx Hs WTX RNA Panel Kit, 2 slides: PN 121500047
NanoString Technologies; CosMx Hs Univ Cell (RNA, 1000 Plex); PN 121500002
NanoString Technologies; CosMx Human 6K Discovery Panel (RNA, 6175 Plex); PN 121500041
Nano electrospray ionization
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]
nESI
NanoString Technologies; CosMx Mouse Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-M-USCP-1KP-R
COMET dataset
Dataset generated from performing the COMET assay.
COMET
Illumina; NovaSeq 6000 SP Reagent v1.5 Kit (300 Cycles); PN 20028400
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
10x Genomics; Chromium i7 Multiplex Kit, 96 rxns; PN 120262
10x Genomics; Chromium Single Cell B Chip Kit, 16 rxns; PN 1000074
Illumina; NovaSeq X Series 25B Reagent Kit (100 Cycle); PN 20125967
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
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
10x Genomics; Chromium Next GEM Single Cell 5' HT Kit v2, 8 rxns; PN 1000374
10x Genomics; Chromium Next GEM Single Cell 5' HT Kit v2, 48 rxns; PN 1000356
10x Genomics; Chromium i7 Multiplex Kit N, Set A, 96 rxn; PN 1000084
10x Genomics; Chromium Single Cell ATAC Library & Gel Bead Kit, 16 rxns; PN 1000110
10x Genomics; Chromium Chip E Single Cell ATAC Kit, 48 rxns; PN 1000155
10x Genomics; Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, 16 rxns; PN 1000175
Illumina; Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit; PN 20034197
Virtual Histology dataset
Dataset generated from performing the Virtual Histology assay.
Virtual Histology
RNA + protein
Raman Imaging dataset
Dataset generated from performing the Raman Imaging assay.
Raman Imaging
STARmap dataset
Dataset generated from performing the STARmap assay.
STARmap
10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome 16 rxns x 16 BC; PN 1000547
Lipid + metabolite + protein
iCLAP dataset
Dataset generated from performing the iCLAP assay.
iCLAP
MACSima dataset
Dataset generated from performing the MACSima assay.
MACSima
10x Genomics; GEM-X Flex Human Transcriptome Probe Kit, 16 samples; PN 1000785
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]
Nuclease-free water
MAPCA (methyl 3-(4-aminophenyl)-2-cyanoacrylate)
10x Genomics; Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit, 16 rxns; PN 1000414
Square binning
Hexagonal binning
Illumina Spatial ver0 dataset
Dataset generated from performing the Illumina Spatial ver0 assay.
Illumina Spatial ver0
NanoString Technologies; GeoMx Human IO Proteome Atlas, 4 slides; PN 121300160
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.
A chemical compound that can re-emit light upon light excitation. [Generated by an AI language model]
Fluorophores
DNA Methylation dataset
Dataset generated from performing the DNA Methylation assay.
DNA Methylation
10x Genomics; Xenium Human Skin Gene Expression Panel; PN 1000643
This is a set of permissible values for 'source storage duration unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'preparation medium' field within the context of the HuBMAP project.
This is a set of permissible values for 'preparation condition' field within the context of the HuBMAP project.
This is a set of permissible values for 'processing time unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'storage medium' field within the context of the HuBMAP project.
This is a set of permissible values for 'storage method' field within the context of the HuBMAP project.
This is a set of permissible values for 'thickness unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'area unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'volume unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'tissue weight unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'pathology distance unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'suspension entity type' field within the context of the HuBMAP project.
This is a set of permissible values for 'dataset type' field within the context of the HuBMAP project.
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.
Dataset type (SenNet)
This is a set of permissible values for 'analyte class' field within the context of the HuBMAP project.
This is a set of permissible values for 'acquisition instrument vendor' field within the context of the HuBMAP project.
This is a set of permissible values for 'acquisition instrument model' field within the context of the HuBMAP project.
This is a set of permissible values for 'time since acquisition instrument calibration unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'stain name' field within the context of the HuBMAP project.
This is a set of permissible values for 'stain technique' field within the context of the HuBMAP project.
This is a set of permissible values for 'preparation instrument vendor' field within the context of the HuBMAP project.
This is a set of permissible values for 'preparation instrument model' field within the context of the HuBMAP project.
This is a set of permissible values for 'tile configuration' field within the context of the HuBMAP project.
This is a set of permissible values for 'scan direction' field within the context of the HuBMAP project.
This is a set of permissible values for 'total run time unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'laterality' field within the context of the HuBMAP project.
This is a set of permissible values for 'organ condition' field within the context of the HuBMAP project.
This is a set of permissible values for 'perfusion solution' field within the context of the HuBMAP project.
This is a set of permissible values for 'transport solution' field within the context of the HuBMAP project.
This is a set of permissible values for 'warm ischemic time unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'cold ischemic time unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'weight unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'height unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'width unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'length unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'library input amount unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'library output amount unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'library concentration unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'library layout' field within the context of the HuBMAP project.
This is a set of permissible values for 'library preparation kit' field within the context of the HuBMAP project.
This is a set of permissible values for 'sample indexing kit' field within the context of the HuBMAP project.
This is a set of permissible values for 'barcode read' field within the context of the HuBMAP project.
This is a set of permissible values for 'UMI read' field within the context of the HuBMAP project.
This is a set of permissible values for 'sequencing reagent kit' field within the context of the HuBMAP project.
This is a set of permissible values for 'transposition reagent kit' field within the context of the HuBMAP project.
This is a set of permissible values for 'transposition method' field within the context of the HuBMAP project.
This is a set of permissible values for 'assay input unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'assay input entity' field within the context of the HuBMAP project.
This is a set of permissible values for 'preparation instrument kit' field within the context of the HuBMAP project.
This is a set of permissible values for 'amount of input analyte unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'mapped area unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'spot size unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'spot spacing unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'permeabilization time unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'RNA probe panel' field within the context of the HuBMAP project.
This is a set of permissible values for 'mass spectrometry ionization technique' field within the context of the HuBMAP project.
This is a set of permissible values for 'mass analysis polarity' field within the context of the HuBMAP project.
This is a set of permissible values for 'ion mobility' field within the context of the HuBMAP project.
This is a set of permissible values for 'mass spectrometry scan mode' field within the context of the HuBMAP project.
This is a set of permissible values for 'matrix deposition method' field within the context of the HuBMAP project.
This is a set of permissible values for 'preparation matrix' field within the context of the HuBMAP project.
This is a set of permissible values for 'desorption solvent' field within the context of the HuBMAP project.
This is a set of permissible values for 'desorption solvent flow rate unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'liquid chromatography instrument vendor' field within the context of the HuBMAP project.
This is a set of permissible values for 'liquid chromatography column vendor' field within the context of the HuBMAP project.
This is a set of permissible values for 'liquid chromatography column length unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'liquid chromatography temperature unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'liquid chromatography inner diameter unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'liquid chromatography flow rate unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'liquid chromatography gradient unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'spatial sampling technique' field within the context of the HuBMAP project.
This is a set of permissible values for 'spatial sampling type' field within the context of the HuBMAP project.
This is a set of permissible values for 'target retrieval incubation time unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'proteinasek incubation time unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'area normalized ion dose unit" field within the context of the HuBMAP project.
This is a set of permissible values for 'pixel dwell time unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'ablation frequency unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'antibody concentration unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'ROI segmentation strategy' field within the context of the HuBMAP project.
This is a set of permissible values for 'Probe hybridization time unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'Oligo probe panel' field within the context of the HuBMAP project.
This is a set of permissible values for 'Derived dataset type' field within the context of the HuBMAP project.
This is a set of permissible values for 'Clonality' field within the context of the HuBMAP project.
This is a set of permissible values for 'antibody reagent kit' field within the context of the HuBMAP project.
This is a set of permissible values for 'viability reagent kit' field within the context of the HuBMAP project.
This is a set of permissible values for 'instrument calibration bead kit' field within the context of the HuBMAP project.
This is a set of permissible values for 'loaded cell concentration unit' field within the context of the HuBMAP project.
This is a set of permissible values for 'Chemistry kit' field within the context of the HuBMAP project.
Sex of the source organism
Sex
If the source was euthanized, select the method of euthanization.
Euthanization method
Hypothermia
Organism was euthanized by gradual cooling to induce deep anesthesia and subsequent euthanasia.
Rapid freezing
Organism was euthanized by rapid freezing in liquid nitrogen.
Inhaled anesthetic euthanasia
Organism was euthanized by inhalation of anesthetic.
A description of the pathogen and opportunist exclusion level of the room where the source is housed.
Room health status
Pathogen free
Organism housed in a room free of pathogens.
Pathogen and opportunist free
Organism housed in a room free of pathogens and opportunistic organisms.
The rack setup type in which the source is housed.
Rack setup
Biocontainment
Organism housed in biocontainment cages designed to prevent the spread of pathogens within and between groups of individual organisms.
Ventilated
Organism housed in ventilated cages providing filtered air directly to the cage.
Micro-Isolator
Organism housed in microisolator cages to protect animals against contamination from the outside environment.
Conventional
Organism housed in cages where the housing environment is not isolated from the animal housing room.
The light cycle in the room where the source is housed.
Light cycle
Longer photoperiods
Organism housed with photoperiods longer that standard/default light cycle.
Reverse light cycles
Organism housed with the lights OFF during the daytime and ON during the nighttime.
The type of cage bedding in the cage where the source is housed.
Bedding
1/4-inch pelleted cellulose
Organism housed with bedding made from 1/4-inch pelleted cellulose.
Refined virgin diced cellulose
Organism housed with bedding made from refined virgin diced cellulose.
Non-contact cage board
Organism housed with bedding made from one of a variety of cage boards.
Wire mesh
Organism housed with bedding made from wire mesh suspended above a collection pan.
Environmental enrichments present in the source’s cage.
Cage enhancements
Nestlets
Organism housed with nesting material made from paper or cotton fibers.
Nest boxes/shelters
Organism housed with man-made enclosures for nesting.
Shelter tubes
Organism housed with man-made tubes for nesting.
Wooden chew sticks
Organism housed with wooden chew sticks for chewing.
Nylon bones
Organism housed with nylon bones for chewing.
An image capture instrument is the device that contains the image detection hardware and signal processing software.
Imaging instrument vendor
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.
Imaging instrument model
This is a set of permissible values for 'image width unit' field.
Image width unit
This is a set of permissible values for 'image height unit' field.
Image height unit
This is a set of permissible values for 'pixel physical size width unit' field.
This is a set of permissible values for 'pixel physical size height unit' field.
This is a set of permissible values for 'pixel physical size depth unit' field.
This is a set of permissible values for 'spacing between slices unit' field or the unit of incremental distance between image slices.
Spacing between slices unit
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.
Imaging frequency unit
Modality
Type of device, process or method used to acquire or derive data.