Files contain raw RNA-seq data associated with spot/slide data.

Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.

Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.

Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc)  from Spatial Transcriptomics.

All data pertaining to the 10X Genomics Xenium In-Situ Hybridization experiment

Processed data files based on Spatial Transcriptomics RNA-seq Level 3.

Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.

The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.

Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.

Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.

Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.

Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.

Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).

The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.

Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).

The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.

HTAN Data File Identifier(s) of the files associated with the accessory content. Should be comma-separated lists.

Free text field containing description of accessory file(s)

Synapse ID of folder containing accessory files

A custom acquisition method [Text - max length 100 characters]

Records the method of acquisition or source for the specimen under consideration.

Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3

State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.

Base sequence of the sequencing adapter. String

Topography not included in the ICD-O-3 Topography codes.

List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...

Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.

The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.

The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.

Age at the time of diagnosis expressed in number of days since birth.

Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.

Numeric value used to describe the average number of alcoholic beverages a person consumes per day.

Indicate if individual has alcohol exposure

A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.

Category to describe the patient's current level of alcohol use as self-reported by the patient.

Read length used for alignment if hard trimming was applied

Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.

Generic name for the workflow used to analyze a data set.

Link to workflow used for read alignment. DockStore.org recommended. String

A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen

The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen

Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.

The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.

Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))

Notes on antibodies replacements and antibody recognition observations.

"Is this antibody acting as a primary or secondary antibody"

The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.

The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.

A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]

The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)

The names of the author(s) of the content presented/published, in the order they appear.

Average base quality collected from samtools. Number

Average insert size collected from samtools. Integer

Average read length collected from samtools. Integer

The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.

A calculated numerical quantity that represents an individual's weight to height ratio.

Presence or absennce of Barretts esophagus goblet cells.

Method that was used to batch correct Level 3 data

Assay that uses beads to target a specific locus on the genome.

Number of sequenced beads. Applies to raw counts matrix only. Integer

The best improvement achieved throughout the entire course of protocol treatment.

The binding density as reported by the application

Is the median count from all probes except the negative control probes. A measure of signal to background for each segment

HTAN biological entity; this can be tissue, blood, analyte and subsamples of those

First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the "dimensions_unit" CDE

Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the "dimensions_unit" CDE

Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the "dimensions_unit" CDE

Whether biotin is used for enriching ligation product

Name of the kit used in bisulfite conversion.

Number of fragments overlapping blacklisted regions

Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.

Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.

Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.

Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.

The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.

Text term to identify assessment tests done in participants during diagnosis

Text term that represents the name of the genomic test performed for breast cancer.

Breast cancer specific attributes in Clinical Data Tier 3

Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.

The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.

Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer

A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer

Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer

Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer

HER2 chromosome 17 ratio in participants with breast cancer

HER2 ratio of the participant at diagnosis

Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer

Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.

Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer

A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer

Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer

Text name of a surgical procedure performed for a person with a diagnosis of breast cancer

The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).

The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.

The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.

Bulk Whole Exome Sequencing aligned files and QC

Bulk Whole Exome Sequencing called variants

Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs

Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.

Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.

Assay types normally determine genomic coverage

The human genome reference used in the alignment of reads

Bulk RNA-seq alignment protocol description

The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.

The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.

Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase

Offset in sequence for cDNA read (in bp): number

Highly-multiplexed plate-based single-cell RNA-Seq assay

The status of central nervous system leukemia at the time of diagnosis.

Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2

Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.

Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder

Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.

The patient's current COVID-19 status of sign or symptom events or interventions

The indicator that describes whether or not a COVID-19 infectious disorder occurred.

The indicator that describes whether or not there was a COVID-19 positive test result.

Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history

Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the "primary_diagnosis" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data.  Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose "Incidence" from the Topic dropdown menu, state of interest from the Area menu, "All Races" from the Race menu, and the cancer type ("Both Sexes" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.

The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as "County, State" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website

Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.

The text term used to describe the source used to determine the patient's cause of death.

The text term used to describe the suspected cause or reason for the patient disease response.

Length of cell barcode read (in bp): number

Offset in sequence for cell barcode read (in bp): number

SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)

Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.

Median number of genes detected per cell. Number

Number of sequenced  cells. Applies to raw counts matrix only.

This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1')

Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details

This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin')

Identify stains that did not pass QC but are included in the dataset.

The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.

The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.

The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.

The average number of cigarettes smoked per day.

Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.

The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.

The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.

The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.

Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.

Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).

Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'

Material Specimen is collected into post procedure

Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).

The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer

The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.

Colorectal cancer specific attributes in Clinical Data Tier 3

The description of the border configuration of a colorectal tumor at pathologic assessment.

Type of adenoma associated with the polyp

A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.

Shape of polyp identified in the participant

Free text field (generally for QC comment)

Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]

The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.

The text term used to describe the method used to diagnose the patient's comorbidity disease.

Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.

An enumerated list of the type of concomitant medication received by the patient.

Fraction of reads coming from cross-sample contamination collected from GATK4. Number

Estimation error of cross-sample contamination collected from GATK4. Number

Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.

The name(s) of the corresponding author(s) of the content presented/published. If more than one corresponding author, please list in the order they appear in the author list.

The ORCiD(s) of the corresponding author(s) of the content presented/published. Should be a valid ORCiD url starting with https://orcid.org/ followed by a 16 digit identifier in dash separated groups of 4 (for example https://orcid.org/0000-0002-1825-0097). If more than one corresponding author, please list ORCiDs in the order the authors appear in the author list.

The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay

A comma separated list of filenames within the CosMx bundle zip file

Indicate if library preparation was based on revived frozen cells.

Reported lung cancer related symptoms person is currently experiencing

Specify the name of a custom alignment workflow

Specify the name of a custom workflow name

Significant pathologic finding present in addition to the cutaneous melanoma.

Text term to indicate presence of tumor at resection margins

Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.

Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.

Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.

The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)

Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.

The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.

Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)

Generic name for the workflow used to analyze a data set

Enzymes and treatment length/temperature for genome digestion

Amount of DNA for library construction, in nanograms.

Number of fragments overlapping with DNase sensitive regions

The digital object identifier (DOI) of the content in the form of https://www.doi.org/{doi} to comply with CrossRef DOI display guidelines.

Represents the percentage of RNA fragments that are >200 nucleotides in size. Number

Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.

Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.

Name of a dataset (e.g. a Synapse folder)

Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable'

Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date the patient's disease progressed. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable'

Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable'

Level	Definition	Example Data
1	Raw sequencing data	FASTQs
2	Aligned primary data	Aligned BAMs
3	Derived biomolecular data mapped to image positions	Barcodes, features, filtered and unfiltered matrices
4	In progress	TBD
Auxiliary	Additional data such as imaging, qc, and json scale factors	TIFF, JPG, PNG, JSON, HTML, etc

HTAN Spatial Transcriptomics