scRNASeq Level 1 Template

A template outlining metadata to use as annotations for scRNA-seq fastq files.

Attribute	Description	Required	Valid Values
Component	A high-level attribute for grouping attributes into templates.	TRUE
Filename	Name of a file. Must be included in DependsOn for all file manifest/annotation templates.	TRUE
fileFormat	Standard file format name or file extension	TRUE	csv, tsv, txt, xlsx, xls, fcs, docx, erate, rec, info, vcf, dose, tbi, fam, bim, bed, bam, h5, mtx, bai, rds, pdf, tgz, zip, fastq, parquet, geojson, tar.gz, h5ad
program	Name of the funding program that supported the generation of data and associated files	TRUE	AMP RA/SLE, AMP AIM, Community Contribution
project	A sub-level attribute of `program` specifying a research initiative working to investigate particular hypotheses.	TRUE	RA, SLE, AIM for RA, STAMP, LOCKIT, V-CoRT, ELLIPSS
resourceType	High-level classification of the file content	TRUE	experimental data, metadata, figure, code
nucleicAcidSource	The source of the nucleic acid used as input for sequencing library fragments. Select all that apply, though in most cases only a single label is expected.	TRUE	poly(A) RNA, rRNA-depleted RNA, gDNA, surface protein feature barcode, intracellular protein feature barcode, antigen capture barcode, multiplexing oligo, BCR mRNA, TCR mRNA, Tn5-accessible gDNA, globin-depleted RNA, CRISPR protospacer feature barcode
libraryPrepMethod	Sequencing library preparation method or kit used to create the library. If no commercially available kit was used, please select 'in-house library prep'.	TRUE	NEBNext Ultra II Directional RNA Library, QIAseq miRNA Library, SMART-Seq v4 Ultra Low Input RNA, Nextera XT, SMARTer Stranded Total RNA v2, Nextera XT DNA, TruSeq Stranded mRNA, SMART-Seq Human BCR with UMI, SMART-Seq Human TCR with UMI, Takara Human BCR profiling for Illumina, Takara Human TCR profiling for Illumina, Takara Human TCRv2 profiling for Illumina, Takara Human scTCR profiling for Illumina, NEBNext Human Immune Sequencing Kit, CEL-Seq2, in-house library prep, Fluidigm C1 HT, 10x Chromium Next GEM Single Cell 3', 10x Chromium Next GEM Single Cell 3' 3.1, 10x Chromium Next GEM Single Cell 5' v2, 10x Chromium GEM-X Single Cell 5' v3, 10x Chromium GEM-X Single Cell 3' v4, 10x GEM-X Universal 5’ Gene Expression v3, 10x GEM-X Flex Gene Expression Human, 10x Chromium Fixed RNA Human Transcriptome, 10x Chromium Single Cell Human TCR, 10x Chromium Single Cell Human BCR, 10x Chromium Next GEM Single Cell ATAC v2, 10x Chromium Next GEM Single Cell 5' v1.1, Chromium Next GEM Single Cell ATAC v1.1, custom DASH-treatment
libraryID	A library label or name, unique within an experiment, used to distinguish sequencing libraries.	FALSE
totalReads	Total number of reads sequenced from the library.	TRUE
platform	The specific version (manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment. Specify where applicable for experimental data files, else enter 'none'. In most cases only a single label is expected, however multiple selections can be provided in comma-delimited list where applicable e.g., for 10x Genomics fastq files please specify both the 10x instrument and the sequencing platform.	FALSE	CyTOF XT, Helios Mass Cytometer, Hyperion, Illumina NextSeq 500, Illumina HiSeq 2500, Illumina NovaSeq 6000, Illumina NovaSeq X, Chromium X, Chromium iX, Chromium Xo, Chromium Controller, Visium CytAssist, Xenium, BD FACSAria Fusion cell sorter, none, Illumina HiSeq X Ten, Chromium Next GEM Chip G, GEM-X OCM 5' Chip, Chromium Next GEM Chip M, Chromium Next GEM Chip Q, Chromium Next GEM Chip H, Chromium GEM-X Single Cell 3' Chip v4, Chromium Next GEM Chip K, GEM-X Flex Gene Expression Chip
sampleProcessingBatch	A label indicating batching of sample processing or preparation that occurs prior to data collection.	FALSE
dataCollectionBatch	A label indicating batching that occurs during data collection, e.g., collecting data across multiple days.	FALSE