scRNA-seq Assay Metadata Template
A template outlining metadata to be collected for each scRNA-seq library in a dataset.
| Attribute | Description | Required | Valid Values |
|---|---|---|---|
| Component | A high-level attribute for grouping attributes into templates. | TRUE | |
| specimenModality | Label assigned to experimental data files indicating whether the data contained corresponds to a single or multiple biospecimens | TRUE | single specimen, multispecimen |
| biospecimenID | A unique identifier assigned to specimens collected from study participants. For multi-specimen data files provide all IDs in a comma-separated list. | TRUE | |
| assay | The technology used to generate the data in this file. For multimodal datasets with concomitant profiling of biospecimen select all assays that apply. e.g., the GEX files from a CITE-seq experiment should be labeled with both 'scRNASeq' and 'CITESeq'. | TRUE | scRNASeq, CyTOF, Xenium, Olink Explore HT, CITESeq, snRNASeq, snATACSeq, RNASeq, multiplexed ELISA, SNP array, imaging mass cytometry, H&E, ASAPSeq, CosMX, serial IHC, imaging mass spectrometry, LC-MS/MS, CE-MS, VDJSeq, scVDJSeq, feature barcode sequencing, SomaScan, WES, WGS, flow cytometry, NULISA |
| libraryID | A library label or name, unique within an experiment, used to distinguish sequencing libraries. | FALSE | |
| 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 |
| 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 |
| totalReads | Total number of reads sequenced from the library. | TRUE | |
| percentCellViability | A measure of the proportion of viable cells within a cell suspension. Scale is 0-100. | 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 |
| sequencingSaturation | A measure of the fraction of library complexity that was sequenced in a library. This metric quantifies the fraction of reads originating from an already-observed UMI. More specifically, this is the fraction of confidently mapped, valid cell-barcode, valid UMI reads that are non-unique. Scale is 0-1. | FALSE | |
| 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 | |
| inputCellCount | An estimate of the number of cells expected to be sequenced in a library. Software that process single-cell sequencing data often include options for users to specify this value to improve processing results. | TRUE |