snRNASeq Assay Metadata Template
A template outlining metadata to be collected for each library in a snRNA-seq dataset.
| Attribute | Description | Required | Valid Values |
|---|---|---|---|
| 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 | 10x Chromium Fixed RNA Human Transcriptome, 10x Chromium GEM-X Single Cell 3' v4, 10x Chromium GEM-X Single Cell 5' v3, 10x Chromium Next GEM Single Cell 3', 10x Chromium Next GEM Single Cell 3' 3.1, 10x Chromium Next GEM Single Cell 5' v1.1, 10x Chromium Next GEM Single Cell 5' v2, 10x Chromium Next GEM Single Cell ATAC v2, 10x Chromium Single Cell Human BCR, 10x Chromium Single Cell Human TCR, 10x GEM-X Flex Gene Expression Human, 10x GEM-X Universal 5? Gene Expression v3, CEL-Seq2, Chromium Next GEM Single Cell ATAC v1.1, Fluidigm C1 HT, NEBNext Human Immune Sequencing Kit, NEBNext Ultra II Directional RNA Library, Nextera XT, Nextera XT DNA, QIAseq miRNA Library, SMART-Seq Human BCR with UMI, SMART-Seq Human TCR with UMI, SMART-Seq v4 Ultra Low Input RNA, SMARTer Stranded Total RNA v2, Takara Human BCR profiling for Illumina, Takara Human TCR profiling for Illumina, Takara Human TCRv2 profiling for Illumina, Takara Human scTCR profiling for Illumina, TruSeq Stranded mRNA, custom DASH-treatment, in-house library prep |
| 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 | ASAPSeq, CE-MS, CITESeq, CosMX, CyTOF, GenePS SeqFISH, H&E, LC-MS/MS, NULISA, Olink Explore HT, Olink Flex, Olink Focus, Olink Reveal, Olink Target 48, Olink Target 96, RNASeq, SNP array, SomaScan, VDJSeq, Visium, WES, WGS, Xenium, feature barcode sequencing, flow cytometry, imaging mass cytometry, imaging mass spectrometry, kiloplex, multiplexed ELISA, scRNASeq, scVDJSeq, serial IHC, snATACSeq, snRNASeq |
| totalReads | Total number of reads sequenced from the library. | True | |
| dataCollectionBatch | A label indicating batching that occurs during data collection, e.g., collecting data across multiple days. | False | |
| Component | A high-level attribute for grouping attributes into templates. | True | |
| percentCellViability | A measure of the proportion of viable cells within a cell suspension. Scale is 0-100. | True | |
| 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 | BCR mRNA, CRISPR protospacer feature barcode, TCR mRNA, Tn5-accessible gDNA, antigen capture barcode, gDNA, globin-depleted RNA, intracellular protein feature barcode, multiplexing oligo, poly(A) RNA, rRNA-depleted RNA, surface protein feature barcode |
| specimenModality | Label assigned to experimental data files indicating whether the data contained corresponds to a single or multiple biospecimens | True | multispecimen, single specimen |
| alignmentReference | The genomic/transcriptomic reference used for performing read alignment against. | True | 10x Cell Ranger Human GRCh38 2020-A, 10x Cell Ranger Human GRCh38 2024-A, modified GRCh38, unknown, vdj_GRCh38_alts_ensembl-4.0.0 |
| sampleProcessingBatch | A label indicating batching of sample processing or preparation that occurs prior to data collection. | 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 | |
| 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 | |
| softwareAndVersion | Relevant software and version used to generate the data file. | False | BD FACSDiva 8.0.1, Cell Ranger 9.0.1, Cell Ranger ATAC v1.1.0, Cell Ranger v3.0.0, Cell Ranger v3.0.1, Cell Ranger v3.0.2, Cell Ranger v3.1.0, Cell Ranger v4.0.0, Cell Ranger v5.0.0, Cell Ranger v5.0.1, Cell Ranger v6.0.0, Cell Ranger v6.0.1, Cell Ranger v6.0.2, Cell Ranger v6.1.0, Cell Ranger v6.1.1, Cell Ranger v6.1.2, Cell Ranger v7.0.0, Cell Ranger v7.0.1, Cell Ranger v7.1.0, Cell Ranger v7.2.0, Cell Ranger v8.0.0, Cell Ranger v8.0.1, Cell Ranger v9.0.0, Space Ranger 3.0.0, Space Ranger 3.0.1, Space Ranger 3.1.0, Space Ranger 3.1.1, Space Ranger 3.1.2, Space Ranger 3.1.3, demuxlet |
| 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. | True | BD FACSAria Fusion cell sorter, BD FACSAria III, BD FACSCanto, BD FACSCanto II, BD FACSDiscover A8, BD FACSDiscover S8, BD FACSLyric Clinical, BD FACSMelody, BD FACSymphony S6, BD LSRFortessa, Chromium Controller, Chromium GEM-X Single Cell 3' Chip v4, Chromium Next GEM Chip G, Chromium Next GEM Chip H, Chromium Next GEM Chip K, Chromium Next GEM Chip M, Chromium Next GEM Chip Q, Chromium X, Chromium Xo, Chromium iX, CyTOF XT, Cytek Aurora, Cytek Aurora Evo, Fluidigm BioMark, GEM-X Flex Gene Expression Chip, GEM-X OCM 5' Chip, Helios Mass Cytometer, Hyperion, Illumina HiSeq 2500, Illumina HiSeq X Ten, Illumina NextSeq 500, Illumina NovaSeq 6000, Illumina NovaSeq X, Not Applicable, Olink Signature Q100, Sony MA900, Thermo Fisher Attune CytPix, Thermo Fisher Attune NxT, Thermo Fisher Attune Xenith, Visium CytAssist, Xenium, none, unknown |
| X10xProbeSetReference | |||
| libraryID | A library label or name, unique within an experiment, used to distinguish sequencing libraries. | True | |
| 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 |