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, zip, 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, Chromium Single Cell Human TCR Amplification Kit, Chromium Single Cell Human BCR Amplification Kit, 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, 10x Chromium 3 GEX, 10x Chromium 3 GEX v3.1, 10x Chromium 5 GEX, 10x Universal 3 GEX, 10x Universal 5 GEX, 10x Chromium Flex, CEL-Seq2, Chromium scATAC Kit v2, in-house library prep, Chromium Next GEM Chip G, Fluidigm C1 HT
libraryID	A library label or name, unique within an experiment, used to distinguish sequencing libraries.	FALSE
batch	A label or identifier that is unique within a given experiment or dataset used to group data related to sample processing, sample pooling, or data collection batches. These batches often introduce technical effects that can be important to account for in downstream analyses.	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, Helios Mass Cytometer, Hyperion, Illumina NovaSeq X, Chromium X, Chromium iX, Chromium Xo, Chromium Controller, Visium CytAssist, Xenium, none