scRNASeq Assay Metadata Template

Template for collecting metadata about scRNA-seq data.

Attribute Description Required Valid Values
Q30_UMI Q30 Bases in UMI; Fraction of bases with Q-score at least 30 in the UMI sequences. This is the R2 read for the Single Cell 3' v1 chemistry and the R1 read for the Single Cell 3' v2 chemistry. TRUE
Q30_bc Fraction of bases with Q-score ≥30 in the cell barcode sequences. This is the i7 index (I1) read for the Single Cell 3' v1 chemistry and the R1 read for the Single Cell 3' v2 chemistry. TRUE
Q30_read Q30 Bases in RNA; Fraction of bases with Q-score at least 30 in the RNA read sequences. This is Illumina R1 for the Single Cell 3' v1 chemistry and Illumina R2 for the Single Cell 3' v2 chemistry. TRUE
alignment_reference The genomic/transcriptomic reference used for performing read alignment against. TRUE 10x Cell Ranger Human GRCh38 2024-A, 10x Cell Ranger Human GRCh38 2020-A
assay The technology used to generate the data. TRUE scRNASeq, RNASeq, WES, WGS, LC-MS/MS, CyTOF
avg_reads_cell total_reads/estimated_cells as calculated by Cell Ranger TRUE
cell_count_1mL Number of cells in 1 mL of suspension TRUE
confident_exonic Fraction of reads that mapped uniquely to an exonic region of the genome TRUE
confident_intergenic Fraction of reads that mapped uniquely to an intergenic region of the genome TRUE
confident_intronic Fraction of reads that mapped uniquely to an intronic region of the genome TRUE
confident_reads Reads mapped confidently to genome; Fraction of reads that mapped uniquely to a genome. A gene mapped to exonic loci from a single gene and also to non-exonic loci is considered uniquely mapped to one of the exonic loci TRUE
confident_transcriptome Reads mapped confidently to transcriptome; Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting TRUE
data_generator Institution that generated the data, i.e. the data processors TRUE BCH, LMU, HSC, MSSM, CSMC, OXF
digestion_cdna_date Date of cDNA digestion YYYY-MM-DD TRUE
estimated_cells Number of cells estimated by Cell Ranger software TRUE
fragment_size_bp Average fragment size of library in base pairs TRUE
genes_detected The number of genes with at least one UMI count in any cell TRUE
gex_con_ng_uL Library concentration ng/uL TRUE
i5_index Illumina-compatible library multiplex barcode TRUE
i7_index Illumina-compatible library multiplex barcode TRUE
library_date Date of library generation YYYY-MM-DD TRUE
library_prep_method 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
median_UMI_cell Total Genes Detected Median UMI Counts per Cell; The number of genes with at least one UMI count in any cell. TRUE
median_genes_cell Median number of read pairs sequenced from the cells assigned to this sample. In case of multiplexing, only cell-associated barcodes assigned exactly one CMO can be assigned to a sample TRUE
percent_cell_viability Percent of viable cells in input cell sample TRUE
platform The specific version (manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment. FALSE HiSeqX, HiSeq4000, Illumina_1M, HiSeq3000, HiSeq2500, DNBSEQ, HiSeq1000, GAIIx, Illumina_h650, ddSEQ Single-Cell Isolator, confocalImaging, Bruker Avance III, Bionano Irys, Biograph mCT, HiSeq2000, Illumina_HumanOmni1-Quadv1.0, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, IlluminaNovaseq6000, IlluminaWholeGenomeDASL, Infinium Global Diversity Array-8, Illumina_Infinium-HumanMethylation450-BeadChip, IlluminaInfiniumGSAMD-24v2-0, IlluminaMethylationEPIC, PacBioRSII, IlluminaHumanMethylation450, IlluminaHumanHT-12_V3_0_R1, IlluminaHumanHap650Yv3_A, IlluminaHumanHap300, Illumina_Omni5-Quad, Biocrates p180, Illumina_Omni2pt5M, Illumina_Omni2.5-8_v1.3, Illumina_Omni2.5-8_v1.1, Illumina_Omni2.5-8, llumina Infinium General Screening Array 24-Kit v3.0, BGISEQ-500, Perlegen300Karray, orbitrap, Xevo TQ-S, Agilent44Karray, NextSeq2000, NextSeq500, NanostringnCounter_MouseADPanel, NanostringnCounter, MiSeq, LTQOrbitrapXL, InfiniumPsychArrayBeadChip, Infinium Omni2.5Exome-8 v1.5, Infinium Omni2.5Exome-8 v1.4, Infinium Omni2.5Exome-8 v1.3, Infinium Omni2.5Exome-8 v1.1, Infinium HumanOmniExpressExome, OrbiTrap Fusion, Orbitrap Fusion Lumos, Olink Target 96, triple quadrupole, PacBio Sequel II, Xevo G2 QTOF, PsychChip, Illumina NovaSeq 6000, Q Exactive HF, Q Exactive, time-of-flight, Simoa HD-1 Analyzer, Signa Premier AIR 3T, IlluminaMiSeq, SequenomMultiplex, quadrupole time-of-flight, Q Exactive Plus
reads_antisense Fraction of reads confidently mapped to the transcriptome, but on the opposite strand of their annotated gene. A read is counted as antisense if it has any alignments that are consistent with an exon of a transcript but antisense to it, and has no sense alignments TRUE
reads_in_cells Fraction of reads from droplets predicted by Cell Ranger to contain a cell TRUE
reads_mapped Fraction of reads that are mapped to the genome TRUE
sample_id Unique sample identifier, formatted as `'individual_id'_'participant_id'_'collection_num'_'type_key'_'sample_num'` TRUE
sequencing_saturation Fraction of reads originating from an already-observed UMI. Is a function of library complexity and sequencing depth calculated as the ratio of the number of confidently-mapped reads with a valid cell-barcode and valid UMI divided by the subset of those reads that had a non-unique combination of cell-barcode, UMI, gene. TRUE
software_and_version Relevant software and version used to collect and process data. TRUE Cell Ranger v9.0.0, Cell Ranger v8.0.1, Cell Ranger v8.0.0, Cell Ranger v7.2.0, Cell Ranger v7.1.0, Cell Ranger v7.0.1, Cell Ranger v7.0.0, Cell Ranger v6.1.2, Cell Ranger v6.1.1, Cell Ranger v6.1.0, Cell Ranger v6.0.2, Cell Ranger v6.0.1, Cell Ranger v6.0.0, Cell Ranger v5.0.1, Cell Ranger v5.0.0, Cell Ranger v4.0.0, Cell Ranger v3.1.0, Cell Ranger v3.0.2, Cell Ranger v3.0.1, Cell Ranger v3.0.0
total_reads Total number of reads in fastq TRUE
valid_UMI Fraction of UMI that match expected whitelist of UMI as calculated by Cell Ranger TRUE
valid_bc Fraction of reads with cell-barcodes that match the whitelist. TRUE
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