scRNA-seq

HTAN scRNA-seq Data Model - Single-cell RNA sequencing data

BaseSequencingAttributes

Minimal base attributes shared across all sequencing types

Attribute	Type	Required	Description
CHECKSUM	string	No	Checksum for data integrity verification
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BaseSequencingLevel1Attributes

Level 1 attributes - sequencing run and library (raw data)

Attribute	Type	Required	Description
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BaseSequencingLevel2Attributes

Level 2 attributes - alignment and alignment workflow

Attribute	Type	Required	Description
GENOMIC_REFERENCE	GenomicReferenceEnum	Yes	Genomic or transcriptomic reference assembly used for alignment. If your genome reference is not among the valid values, please contact your data liaison.
GENOMIC_REFERENCE_URL	string	Yes	URL to genomic or transcriptomic reference
GENOME_ANNOTATION_URL	string	Yes	URL to genome or transcriptome annotation
WORKFLOW_VERSION	string	Yes	Major version of the workflow, or ‘Not applicable’ when no workflow version applies.
WORKFLOW_LINK	string	Yes	Link to workflow or command. DockStore.org recommended
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BaseSequencingLevel3Attributes

Level 3+ attributes - inherits alignment and workflow; used for processed/analysis levels

Attribute	Type	Required	Description
GENOMIC_REFERENCE	GenomicReferenceEnum	Yes	Genomic or transcriptomic reference assembly used for alignment. If your genome reference is not among the valid values, please contact your data liaison.
GENOMIC_REFERENCE_URL	string	Yes	URL to genomic or transcriptomic reference
GENOME_ANNOTATION_URL	string	Yes	URL to genome or transcriptome annotation
WORKFLOW_VERSION	string	Yes	Major version of the workflow, or ‘Not applicable’ when no workflow version applies.
WORKFLOW_LINK	string	Yes	Link to workflow or command. DockStore.org recommended
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

scRNALevel1

scRNA-seq Level 1 data - Raw sequencing files and metadata

Attribute	Type	Required	Description
FILE_FORMAT	string	Yes	Format of the raw sequencing file (fastq or fastq.gz)
FILENAME	string	Yes	Name of the file. Must end with an extension matching the FILE_FORMAT (.fastq for fastq; .fastq.gz or .fq.gz for fastq.gz)
SINGLE_CELL_ISOLATION_METHOD	SingleCellIsolationMethodEnum	Yes	Method used to isolate single cells
DISSOCIATION_METHOD	DissociationMethodEnum	Yes	Method used to dissociate tissue into single cells
CRYOPRESERVED_CELLS_IN_SAMPLE	boolean	No	Whether cells were cryopreserved in the sample
NUCLEIC_ACID_SOURCE	NucleicAcidSourceEnum	Yes	Type of nucleic acid used for sequencing
LIBRARY_CONSTRUCTION_METHOD	LibraryConstructionMethodEnum	Yes	Method used to construct the sequencing library
REVERSE_TRANSCRIPTION_PRIMER	ReverseTranscriptionPrimerEnum	Yes	Primer used for reverse transcription
SPIKE_IN	SpikeInEnum	Yes	Type of spike-in used, if any
READ_INDICATOR	ReadIndicatorEnum	Yes	Type of read (forward, reverse, index)
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

scRNALevel2

scRNA-seq Level 2 data - Workflow and processing metadata

Attribute	Type	Required	Description
FILE_FORMAT	string	Yes	Format of the aligned file (bam or cram)
FILENAME	string	Yes	Name of the file. Must end with an extension matching the FILE_FORMAT (.bam for bam; .cram for cram)
SCRNASEQ_WORKFLOW_TYPE	scRNAseqWorkflowTypeEnumLevel2	Yes	Generic name for the workflow used to analyze the dataset
WHITELIST_CELL_BARCODE_FILE_LINK	string	No	Link to whitelist cell barcode file
CELL_BARCODE_TAG	string	No	Tag used for cell barcodes
UMI_TAG	string	No	Tag used for UMIs
GENOMIC_REFERENCE	GenomicReferenceEnum	Yes	Genomic or transcriptomic reference assembly used for alignment. If your genome reference is not among the valid values, please contact your data liaison.
GENOMIC_REFERENCE_URL	string	Yes	URL to genomic or transcriptomic reference
GENOME_ANNOTATION_URL	string	Yes	URL to genome or transcriptome annotation
WORKFLOW_VERSION	string	Yes	Major version of the workflow, or ‘Not applicable’ when no workflow version applies.
WORKFLOW_LINK	string	Yes	Link to workflow or command. DockStore.org recommended
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

CoreFileAttributes

Universal attributes that apply to all file-based data in HTAN

Attribute	Type	Required	Description
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

scRNALevel3and4

Single-cell RNA-seq Level 3 and 4 - Gene expression files and cell relationships

Attribute	Type	Required	Description
FILE_FORMAT	string	Yes	Format of the file (only h5ad files accepted for Level 3/4)
FILENAME	string	Yes	Name of the file. Must end with .h5ad extension
SCRNASEQ_WORKFLOW_TYPE	scRNAseqWorkflowTypeEnumLevel3and4	Yes	Generic name for the workflow used to analyze a data set
SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION	string	Yes	Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion
DATA_CATEGORY	DataCategoryEnum	Yes	Specific content type of the data file
MATRIX_TYPE	MatrixTypeEnum	Yes	Type of data stored in matrix
LINKED_MATRICES	string	No	All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames
CELL_MEDIAN_NUMBER_READS	integer	Yes	Median number of reads per cell
CELL_MEDIAN_NUMBER_GENES	integer	Yes	Median number of genes detected per cell
CELL_TOTAL	integer	Yes	Number of sequenced cells. Applies to raw counts matrix only
ANNDATA_SCHEMA_VERSION	string	Yes	Version of AnnData schema (must be 0.1 for CellxGene compliance)
ANNDATA_STRUCTURE_VALIDATED	boolean	Yes	Whether the h5ad file structure has been validated against AnnData 0.1 schema
GENOMIC_REFERENCE	GenomicReferenceEnum	Yes	Genomic or transcriptomic reference assembly used for alignment. If your genome reference is not among the valid values, please contact your data liaison.
GENOMIC_REFERENCE_URL	string	Yes	URL to genomic or transcriptomic reference
GENOME_ANNOTATION_URL	string	Yes	URL to genome or transcriptome annotation
WORKFLOW_VERSION	string	Yes	Major version of the workflow, or ‘Not applicable’ when no workflow version applies.
WORKFLOW_LINK	string	Yes	Link to workflow or command. DockStore.org recommended
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

Enums

DataCategoryEnum

Value	Description
Exon Expression Quantification	Exon expression quantification
Gene Expression	Gene expression data
Gene Expression Quantification	Gene expression quantification
Isoform Expression Quantification	Isoform expression quantification
Other	Other data category
Splice Junction Quantification	Splice junction quantification
Transcript Expression	Transcript expression data

DissociationMethodEnum

Value	Description
Enzymatic	Enzymatic dissociation method
Mechanical	Mechanical dissociation method
Other	Other dissociation method
Unknown	Unknown dissociation method

GenomicReferenceEnum

Genomic or transcriptomic reference assembly used for alignment

Value	Description
GRCh37	Genome Reference Consortium human build 37
GRCh37.p13	GRCh37 patch release 13
GRCh38	Genome Reference Consortium human build 38
GRCh38.p13	GRCh38 patch release 13
GRCh38.p14	GRCh38 patch release 14
hg19	UCSC human genome reference hg19
hg38	UCSC human genome reference hg38

LibraryConstructionMethodEnum

Value	Description
10X Genomics	10X Genomics library construction method
Drop-seq	Drop-seq library construction method
Fluidigm C1	Fluidigm C1 library construction method
InDrop	InDrop library construction method
Other	Other library construction method
Smart-seq	Smart-seq library construction method
Unknown	Unknown library construction method

LibraryLayoutEnum

Value	Description
Paired-end	Paired-end sequencing
Single-end	Single-end sequencing

MatrixTypeEnum

Value	Description
Batch Corrected Counts	Batch corrected count matrix
Normalized Counts	Normalized count matrix
Raw Counts	Raw count matrix
Scaled Counts	Scaled count matrix

NucleicAcidSourceEnum

Value	Description
DNA	DNA nucleic acid source
RNA	RNA nucleic acid source
Unknown	Unknown nucleic acid source

ReadIndicatorEnum

Value	Description
Forward	Forward read indicator
Index	Index read indicator
Reverse	Reverse read indicator
Unknown	Unknown read indicator

ReverseTranscriptionPrimerEnum

Value	Description
Oligo-dT	Oligo-dT reverse transcription primer
Random Hexamer	Random hexamer reverse transcription primer
Unknown	Unknown reverse transcription primer

SequencingPlatformEnum

Value	Description
ABI_SOLID	ABI SOLID sequencing platform
BGISEQ	BGI sequencing platform
CAPILLARY	Capillary sequencing platform
COMPLETE_GENOMICS	Complete Genomics sequencing platform
HELICOS	Helicos sequencing platform
ILLUMINA	Illumina sequencing platform
ION_TORRENT	Ion Torrent sequencing platform
LS454	454 sequencing platform
OXFORD_NANOPORE	Oxford Nanopore sequencing platform
PACBIO_SMRT	PacBio SMRT sequencing platform

SingleCellIsolationMethodEnum

Value	Description
Cell Sorting	Cell sorting isolation method
Droplet-based	Droplet-based isolation method
Manual Picking	Manual picking isolation method
Microfluidics	Microfluidics isolation method
Other	Other isolation method
Unknown	Unknown isolation method

SpikeInEnum

Value	Description
ERCC	ERCC spike-in
None	No spike-in
Other	Other spike-in
Unknown	Unknown spike-in

scRNAseqWorkflowTypeEnumLevel2

Value	Description
CellRanger	CellRanger workflow
HCA Optimus	HCA Optimus workflow
Other	Other workflow
SEQC	SEQC workflow
STARsolo	STARsolo workflow
Unknown	Unknown workflow
dropEST	dropEST workflow

scRNAseqWorkflowTypeEnumLevel3and4

Value	Description
Cell annotation	Cell annotation workflow
CellRanger	10x Genomics CellRanger workflow
Cufflinks	Cufflinks workflow
DEXSeq	DEXSeq workflow
Differentiation trajectory analysis	Differentiation trajectory analysis workflow
HCA Optimus	Human Cell Atlas Optimus workflow
HTSeq - FPKM	HTSeq FPKM workflow
Other	Other workflow type
SEQC	SEQC workflow
STARsolo	STARsolo alignment workflow
dropEST	dropEST workflow