Attribute Manifest Name Description Required Conditional If Data Type Valid Values Filename scRNA-seq Level 1,scRNA-seq Level 2,scRNA-seq Level 3,scRNA-seq Level 4,scDNA-seq Level 1,scDNA-seq Level 2,scATAC-seq Level 1,scATAC-seq Level 2,scATAC-seq Level 3,scATAC-seq Level 4,scmC-seq Level 1,scmC-seq Level 2,Bulk WES Level 1,Bulk WES Level 2,Bulk WES Level 3,Bulk Methylation-seq Level 1,Bulk Methylation-seq Level 2,Bulk Methylation-seq Level 3,Bulk RNA-seq Level 1,Bulk RNA-seq Level 2,Bulk RNA-seq Level 3,HI-C-seq Level 1,HI-C-seq Level 2,HI-C-seq Level 3 Name of a file True String File Format scRNA-seq Level 1,scRNA-seq Level 2,scRNA-seq Level 3,scRNA-seq Level 4,scDNA-seq Level 1,scDNA-seq Level 2,scATAC-seq Level 1,scATAC-seq Level 2,scATAC-seq Level 3,scATAC-seq Level 4,scmC-seq Level 1,scmC-seq Level 2,Bulk WES Level 1,Bulk WES Level 2,Bulk WES Level 3,Bulk Methylation-seq Level 1,Bulk Methylation-seq Level 2,Bulk Methylation-seq Level 3,Bulk RNA-seq Level 1,Bulk RNA-seq Level 2,Bulk RNA-seq Level 3,HI-C-seq Level 1,HI-C-seq Level 2,HI-C-seq Level 3 Format of a file (e.g. txt, csv, fastq, bam, etc.) True String hdf5 bedgraph idx idat bam bai excel powerpoint tif tiff OME-TIFF png doc pdf fasta fastq sam vcf bcf maf bed chp cel sif tsv csv txt plink bigwig wiggle gct bgzip zip seg html mov hyperlink svs Md flagstat gtf raw msf rmd bed narrowPeak bed broadPeak bed gappedPeak avi pzfx fig xml tar R script abf bpm dat jpg locs Sentrix descriptor file Python script sav gzip sdf RData hic ab1 7z gff3 json sqlite svg sra recal tranches mtx tagAlign dup DICOM czi mex cloupe Am cell am mpg M mzML scn dcc rcc pkc sf bedpe HTAN Parent Biospecimen ID scRNA-seq Level 1,scDNA-seq Level 1,scATAC-seq Level 1,scmC-seq Level 1,Bulk WES Level 1,Bulk Methylation-seq Level 1,Bulk RNA-seq Level 1,HI-C-seq Level 1,scRNA-seq Level 2 HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated True Is lowest level is "Yes - Is lowest level" String HTAN Data File ID scRNA-seq Level 1,scRNA-seq Level 2,scRNA-seq Level 3,scRNA-seq Level 4,scDNA-seq Level 1,scDNA-seq Level 2,scATAC-seq Level 1,scATAC-seq Level 2,scATAC-seq Level 3,scATAC-seq Level 4,scmC-seq Level 1,scmC-seq Level 2,Bulk WES Level 1,Bulk WES Level 2,Bulk WES Level 3,Bulk Methylation-seq Level 1,Bulk Methylation-seq Level 2,Bulk Methylation-seq Level 3,Bulk RNA-seq Level 1,Bulk RNA-seq Level 2,Bulk RNA-seq Level 3,HI-C-seq Level 1,HI-C-seq Level 2,HI-C-seq Level 3 Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz) True String Nucleic Acid Source scRNA-seq Level 1,scDNA-seq Level 1,scATAC-seq Level 1,scmC-seq Level 1,Bulk Methylation-seq Level 1,Bulk RNA-seq Level 1,HI-C-seq Level 1 The source of the input nucleic molecule True String Single Cell Bulk Whole Cell Single Nucleus Bulk Nuclei Micro-region Cryopreserved Cells in Sample scRNA-seq Level 1 Indicate if library preparation was based on revived frozen cells. True String yes no Single Cell Isolation Method scRNA-seq Level 1,scATAC-seq Level 1,scmC-seq Level 1 The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets) True String Microfluidics Chip Droplets FACS Plates 10x Nuclei Isolation Dissociation Method scRNA-seq Level 1,scATAC-seq Level 1 The tissue dissociation method used for scRNASeq or scATAC-seq assays True String gentleMACS Dounce Enzymatic Digestion Not Applicable Library Construction Method scRNA-seq Level 1,scATAC-seq Level 1 Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711] True String Smart-seq2 Smart-SeqV4 10xV1.0 10xV1.1 10xV2 10xV3 10xV3.1 CEL-seq2 Drop-seq inDropsV2 inDropsV3 TruDrop sci-ATAC-seq Nextera XT 10x Multiome 10x FLEX 10x GEM 3' 10x GEM 5' Read Indicator scRNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads 1 (I1), Index Reads 2 (I2), or Other True String R1 R2 R1&R2 I1 I2 Other Read1 scRNA-seq Level 1 Read 1 content description True String Cell Barcode and UMI cDNA Read2 scRNA-seq Level 1 Read 2 content description True String Cell Barcode and UMI cDNA End Bias scRNA-seq Level 1 The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript True String 3 Prime 5 Prime Full Length Transcript Reverse Transcription Primer scRNA-seq Level 1 An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA True String Oligo-dT Poly-dT Feature barcoding Random Spike In scRNA-seq Level 1,Bulk RNA-seq Level 1 A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix True String ERCC Other Spike In No Spike In PhiX Sequencing Platform scRNA-seq Level 1,scATAC-seq Level 1,scmC-seq Level 1,Bulk WES Level 1,Bulk Methylation-seq Level 1,Bulk RNA-seq Level 1,HI-C-seq Level 1 A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument. True String Illumina Next Seq 500 Illumina Next Seq 550 Illumina Next Seq 2500 Illumina NovaSeq 6000 Illumina MiSeq 454 GS FLX Titanium AB SOLiD 4 AB SOLiD 2 AB SOLiD 3 Complete Genomics Illumina HiSeq X Ten Illumina HiSeq X Five Illumina Genome Analyzer II Illumina Genome Analyzer IIx Illumina HiSeq 2000 Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina NextSeq Ion Torrent PGM Ion Torrent Proton Ion Torrent S5 PacBio RS NovaSeq 6000 NovaSeqS4 Ultima Genomics UG100 Oxford Nanopore minION GridION PromethION PacBio Sequel2 Revio Illumina NextSeq 1000 Illumina NextSeq 2000 Other unknown Not Reported Total Number of Input Cells scRNA-seq Level 1 Number of cells loaded/placed on plates True String Input Cells and Nuclei scRNA-seq Level 1 Number of cells and number of nuclei input; entry format: number, number True String Library Preparation Days from Index scRNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable' False String Single Cell Dissociation Days from Index scRNA-seq Level 1 Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable' True String Sequencing Library Construction Days from Index scRNA-seq Level 1 Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable' True String Nucleic Acid Capture Days from Index scRNA-seq Level 1 Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable' True String Protocol Link scRNA-seq Level 1,scATAC-seq Level 1,HI-C-seq Level 1 Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated. True String Technical Replicate Group scRNA-seq Level 1,scATAC-seq Level 1,scmC-seq Level 1,HI-C-seq Level 1 A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch) False String Empty Well Barcode scRNA-seq Level 1 Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays. True Library Construction Method is "CEL-seq2" String Well Index scRNA-seq Level 1 Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays False Library Construction Method is "CEL-seq2" String yes no Feature Reference Id scRNA-seq Level 1 Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref] True Reverse Transcription Primer is "Feature barcoding" String UMI Barcode Offset scRNA-seq Level 1 Start position of UMI barcode in the sequence. Values: number, 0 for start of read True Spatial Read2 is "Spatial Barcode and UMI" String UMI Barcode Length scRNA-seq Level 1 Length of UMI barcode read (in bp): number True Spatial Read2 is "Spatial Barcode and UMI" String Cell Barcode and UMI scRNA-seq Level 1,scmC-seq Level 1 Cell and transcript identifiers False String Median UMIs per Cell Number scRNA-seq Level 1 Number True Read2 is "Cell Barcode and UMI" String Cell Barcode Offset scRNA-seq Level 1 Offset in sequence for cell barcode read (in bp): number True Read2 is "Cell Barcode and UMI" String Cell Barcode Length scRNA-seq Level 1 Length of cell barcode read (in bp): number True Read2 is "Cell Barcode and UMI" String Valid Barcodes Cell Number scRNA-seq Level 1 Number True Read2 is "Cell Barcode and UMI" String CEL-seq2 scRNA-seq Level 1 Highly-multiplexed plate-based single-cell RNA-Seq assay False String Feature barcoding scRNA-seq Level 1 A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc] False String HTAN Parent Data File ID scRNA-seq Level 2,scRNA-seq Level 3,scRNA-seq Level 4,scDNA-seq Level 2,scATAC-seq Level 2,scATAC-seq Level 3,scATAC-seq Level 4,scmC-seq Level 2,Bulk WES Level 2,Bulk WES Level 3,Bulk Methylation-seq Level 2,Bulk Methylation-seq Level 3,Bulk RNA-seq Level 2,Bulk RNA-seq Level 3,HI-C-seq Level 2,HI-C-seq Level 3 HTAN Data File Identifier indicating the file(s) from which these files were derived True String scRNAseq Workflow Type scRNA-seq Level 2,scRNA-seq Level 3,scRNA-seq Level 4 Generic name for the workflow used to analyze a data set. True String CellRanger STARsolo HCA Optimus dropEST SEQC Cufflinks DEXSeq HTSeq - FPKM Cell annotation Differentiation trajectory analysis Other Workflow Version scRNA-seq Level 2,scRNA-seq Level 3,scRNA-seq Level 4,scATAC-seq Level 4 Major version of the workflow (e.g. Cell Ranger v3.1) True String scRNAseq Workflow Parameters Description scRNA-seq Level 2,scRNA-seq Level 3,scRNA-seq Level 4 Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion True String Workflow Link scRNA-seq Level 2,scRNA-seq Level 3,scRNA-seq Level 4,scATAC-seq Level 4,Bulk RNA-seq Level 3 Link to workflow or command. DockStore.org recommended. URL True Pseudo Alignment Used is "Yes - Pseudo Alignment Used" String Genomic Reference scRNA-seq Level 2,scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk WES Level 3,Bulk RNA-seq Level 2,HI-C-seq Level 1,HI-C-seq Level 2,HI-C-seq Level 3,Bulk RNA-seq Level 3 Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39) True Pseudo Alignment Used is "Yes - Pseudo Alignment Used" String Genomic Reference URL scRNA-seq Level 2,scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk WES Level 3,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2,Bulk RNA-seq Level 3 Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) True Pseudo Alignment Used is "Yes - Pseudo Alignment Used" String Genome Annotation URL scRNA-seq Level 2 Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz) True String Checksum scRNA-seq Level 2 MD5 checksum of the BAM file True String Whitelist Cell Barcode File Link scRNA-seq Level 2 Link to file listing all possible cell barcodes. URL True String Cell Barcode Tag scRNA-seq Level 2 SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z) True String UMI Tag scRNA-seq Level 2 SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z) True String Applied Hard Trimming scRNA-seq Level 2 Was Hard Trimming applied True String Yes - Applied Hard Trimming no Is lowest level scRNA-seq Level 2,Bulk WES Level 2,Bulk RNA-seq Level 2 Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing False String Yes - Is lowest level no Yes - Is lowest level scRNA-seq Level 2 If manifest is lowest level require HTAN Parent Biospecimen ID False String Data Category scRNA-seq Level 3,Bulk RNA-seq Level 3 Specific content type of the data file. True String Gene Expression Transcript Expression Exon Expression Quantification Gene Expression Quantification Isoform Expression Quantification Splice Junction Quantification Other Matrix Type scRNA-seq Level 3,Bulk RNA-seq Level 3 Type of data stored in matrix. True String Raw Counts Normalized Counts Scaled Counts Batch Corrected Counts Linked Matrices scRNA-seq Level 3 All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames False String Cell Median Number Reads scRNA-seq Level 3 Median number of reads per cell. Number True String Cell Median Number Genes scRNA-seq Level 3 Median number of genes detected per cell. Number True String Cell Total scRNA-seq Level 3 Number of sequenced cells. Applies to raw counts matrix only. True String Sequencing Batch ID scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Links samples to a specific local sequencer run. Can be string or 'null' True String Library Layout scDNA-seq Level 1,scmC-seq Level 1,Bulk WES Level 1,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 1 Sequencing read type True String Paired End Single Read Mid-length Long Read Library Selection Method scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 How RNA molecules are isolated. True String Hybrid Selection PCR Affinity Enrichment Poly-T Enrichment Random rRNA Depletion miRNA Size Fractionation Other Read Length scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 The length of the sequencing reads. Can be integer, null True String Library Preparation Kit Name scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Name of Library Preparation Kit. String True String Library Preparation Kit Vendor scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Vendor of Library Preparation Kit. String True String Library Preparation Kit Version scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Version of Library Preparation Kit. String True String Adapter Name scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Name of the sequencing adapter. String False String Adapter Sequence scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Base sequence of the sequencing adapter. String False String Base Caller Name scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Name of the base caller. String False String Base Caller Version scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Version of the base caller. String False String Flow Cell Barcode scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Flow cell barcode. Wrong or missing information may affect analysis results. String False String Fragment Maximum Length scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer False String Fragment Mean Length scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number False String Fragment Minimum Length scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer False String Fragment Standard Deviation Length scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number False String Lane Number scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer False String Library Strand scDNA-seq Level 1,Bulk RNA-seq Level 1 Library stranded-ness. False String Unstranded First Stranded Second Stranded Not Applicable Multiplex Barcode scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 The barcode/index sequence used. Wrong or missing information may affect analysis results. String False String Size Selection Range scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Range of size selection. String False String Target Depth scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 The targeted read depth prior to sequencing. Integer False String To Trim Adapter Sequence scDNA-seq Level 1,Bulk WES Level 1,Bulk RNA-seq Level 1 Does the user suggest adapter trimming? False String Yes - Trim Adapter Sequence no Adapter Content scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Basic Statistics scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Encoding scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 Version of ASCII encoding of quality values found in the file. String False String Kmer Content scDNA-seq Level 1,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Overrepresented Sequences scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Per Base N Content scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Per Base Sequence Content scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Per Base Sequence Quality scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Per Sequence GC Content scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Per Sequence Quality Score scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Per Tile Sequence Quality scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Percent GC Content scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 The overall %GC of all bases in all sequences. Integer False String Sequence Duplication Levels scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Sequence Length Distribution scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 State classification given by FASTQC for the metric. Metric specific details about the states are available on their website. False String FAIL PASS WARN unknown Not Reported Total Reads scDNA-seq Level 1,scDNA-seq Level 2,scATAC-seq Level 1,scATAC-seq Level 2,scmC-seq Level 1,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 1,Bulk RNA-seq Level 2,HI-C-seq Level 1 Total number of reads per sample. Integer False String QC Workflow Type scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 Generic name for the workflow used to analyze a data set. String False String QC Workflow Version scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 Major version for a workflow. String False String QC Workflow Link scDNA-seq Level 1,Bulk WES Level 2,Bulk RNA-seq Level 1 Link to workflow used. String False String Alignment Workflow Url scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Link to workflow used for read alignment. DockStore.org recommended. String True String Alignment Workflow Type scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Generic name for the workflow used to analyze a data set. True String BWA BWA with BQSR BWA-aln BWA-mem BWA with Mark Duplicates and BQSR STAR 2-Pass STAR 2-Pass Chimeric STAR 2-Pass Genome STAR 2-Pass Transcriptome Bowtie Bismark GSNAP BSMAP BSmooth BS-Seeker2 BS-Seeker RMAP MethylCoder BRAT-BW Pash Segemehl Bisulfighter BatMeth LAST ERNE-BS5 B-SOLANA SOCS-B BWA-meth Other Alignment Workflow None Index File Name scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 The name (or part of a name) of a file (of any type). String True String Average Base Quality scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Average base quality collected from samtools. Number False String Average Insert Size scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Average insert size collected from samtools. Integer False String Average Read Length scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Average read length collected from samtools. Integer False String Mean Coverage scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number False String Pairs On Diff CHR scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Pairs on different chromosomes collected from samtools. Integer False String Proportion Reads Mapped scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Proportion of mapped reads collected from samtools. Number False String MapQ30 scDNA-seq Level 2,scATAC-seq Level 1,scATAC-seq Level 2 Number of reads with Quality >= 30. False String Total Uniquely Mapped scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Number of reads that map to genome. Integer False String Total Unmapped reads scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Number of reads that did not map to genome. Integer False String Proportion Reads Duplicated scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Proportion of duplicated reads collected from samtools. Number False String Short Reads scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Number of reads that were too short. Integer False String Proportion Coverage 10x scDNA-seq Level 2,scATAC-seq Level 2,Bulk WES Level 2 Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools. False String Proportion Coverage 30X scDNA-seq Level 2,scATAC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2 Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools. False String Proportion Targets No Coverage scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number False String Proportion Base Mismatch scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Proportion of mismatched bases collected from samtools. Number False String Proportion Mitochondrial Reads scDNA-seq Level 2 Proportion of reads mapping to mitochondria. False String Contamination scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Fraction of reads coming from cross-sample contamination collected from GATK4. Number False String Contamination Error scDNA-seq Level 2,scATAC-seq Level 2,scmC-seq Level 2,Bulk WES Level 2,Bulk Methylation-seq Level 2,Bulk RNA-seq Level 2 Estimation error of cross-sample contamination collected from GATK4. Number False String Single Nucleus Buffer scATAC-seq Level 1,scmC-seq Level 1 Nuclei isolation buffer True String NIB 10x Omni TST Transposition Reaction scATAC-seq Level 1,HI-C-seq Level 1 Name of the transposase, transposon sequences True String Tn5 EZ-Tn5 Tn5-059 Nextera Tn5 Diagenode-unloaded Apex-Bio Diagenode-loaded Apex-Bio In-House scATACseq Library Layout scATAC-seq Level 1 Sequencing read type True String scATACseq Paired End Nucleus Identifier scATAC-seq Level 1,scmC-seq Level 1 Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from True String Nuclei Barcode Nuclei Barcode Length scATAC-seq Level 1 Nuclei Barcode Length True String Nuclei Barcode Read scATAC-seq Level 1 Nuclei Barcode Read True String scATACseq Read1 scATAC-seq Level 1 Read 1 content description True String Cell Barcode and DNA Insert Sample Index and DNA Insert DNA Insert Sample Index Cell Barcode scATACseq Read2 scATAC-seq Level 1 Read 2 content description True String Cell Barcode and DNA Insert Sample Index and DNA Insert DNA Insert Sample Index Cell Barcode scATACseq Read3 scATAC-seq Level 1 Read 3 content description False String Cell Barcode and DNA Insert Sample Index and DNA Insert DNA Insert Sample Index Cell Barcode Threshold for Minimum Passing Reads scATAC-seq Level 1,scmC-seq Level 1 Threshold for calling cells True String Total Number of Passing Nuclei scATAC-seq Level 1,scmC-seq Level 1 Number of nuclei sequenced True String Median Fraction of Reads in Peaks scATAC-seq Level 1,scmC-seq Level 1 Median fraction of reads in peaks (FRIP) True String Median Fraction of Reads in Annotated cis DNA Elements scATAC-seq Level 1 Median fraction of reads in annotated cis-DNA elements (FRIADE) True String Median Passing Read Percentage scATAC-seq Level 1,scmC-seq Level 1 Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode True String Median Percentage of Mitochondrial Reads per Nucleus scATAC-seq Level 1,scATAC-seq Level 2,scmC-seq Level 1 Contamination from mitochondrial sequences True String Peaks Calling Software scATAC-seq Level 1,scmC-seq Level 1 Generic name of peaks calling tool True String Nuclei Barcode scATAC-seq Level 1 Nuclei Barcode False String Nuclei Barcode Read Nuclei Barcode Length scATACseq Paired End scATAC-seq Level 1 A library layout type False String scATACseq Read1 scATACseq Read2 nCount Peaks scATAC-seq Level 2,scATAC-seq Level 3 Total number of fragments in peaks False String nFeature Peaks scATAC-seq Level 2,scATAC-seq Level 3 Number of peaks with at least one read False String Total Read-Pairs scATAC-seq Level 2,scATAC-seq Level 3 Total read-pairs False String Duplicate Read-Pairs scATAC-seq Level 2,scATAC-seq Level 3 Number of duplicate read-pairs False String Chimeric Read-Pairs scATAC-seq Level 2,scATAC-seq Level 3 Number of chimerically mapped read-pairs False String Unmapped Read-Pairs scATAC-seq Level 2,scATAC-seq Level 3 Number of read-pairs with at least one end not mapped False String LowMapQ scATAC-seq Level 2,scATAC-seq Level 3 Number of read-pairs with <30 mapq on at least one end False String Mitochondrial Read-Pairs scATAC-seq Level 2,scATAC-seq Level 3 Number of read-pairs mapping to mitochondria and non-nuclear contigs False String Passed Filters scATAC-seq Level 2,scATAC-seq Level 3 Number of non-duplicate, usable read-pairs i.e. fragments False String TSS Fragments scATAC-seq Level 2,scATAC-seq Level 3 Number of fragments overlapping with TSS regions False String DNase Sensitive Region Fragments scATAC-seq Level 2,scATAC-seq Level 3 Number of fragments overlapping with DNase sensitive regions False String Enhancer Region Fragments scATAC-seq Level 2,scATAC-seq Level 3 Number of fragments overlapping enhancer regions False String Promoter Region Fragments scATAC-seq Level 2,scATAC-seq Level 3 Number of fragments overlapping promoter regions False String On Target Fragments scATAC-seq Level 2,scATAC-seq Level 3 Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity) False String Blacklist Region Fragments scATAC-seq Level 2,scATAC-seq Level 3 Number of fragments overlapping blacklisted regions False String Peak Region Fragments scATAC-seq Level 2,scATAC-seq Level 3 Number of fragments overlapping peaks False String Peak Region Cutsites scATAC-seq Level 2,scATAC-seq Level 3 Number of ends of fragments in peak regions False String Nucleosome Signal scATAC-seq Level 2,scATAC-seq Level 3 Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free)) False String Nucleosome Percentile scATAC-seq Level 2,scATAC-seq Level 3 Percentile rank of nucleosome score False String TSS Enrichment scATAC-seq Level 2,scATAC-seq Level 3 Transcription start site (TSS) enrichment score False String TSS Percentile scATAC-seq Level 2,scATAC-seq Level 3 Percentile rank of TSS score False String Pct Reads in Peaks scATAC-seq Level 2,scATAC-seq Level 3 Percentage of reads in peaks False String Blacklist Ratio scATAC-seq Level 2,scATAC-seq Level 3 Ratio of reads in blacklist regions False String Seurat Clusters scATAC-seq Level 2,scATAC-seq Level 3 Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm False String nCount RNA scATAC-seq Level 2,scATAC-seq Level 3 Total number of fragments in genes False String nFeature RNA scATAC-seq Level 2,scATAC-seq Level 3 Number of genes detected in cell False String MACS2 Seqnames scATAC-seq Level 2,scATAC-seq Level 3 Chromosome id False String MACS2 Start scATAC-seq Level 2,scATAC-seq Level 3 Genomic starting position in MACS2 False String MACS2 End scATAC-seq Level 2,scATAC-seq Level 3 Genomic ending position in MACS2 False String MACS2 Width scATAC-seq Level 2,scATAC-seq Level 3 Width of the peak in bases in MACS2 False String MACS2 Strand scATAC-seq Level 2,scATAC-seq Level 3 DNA stand aligned with in MACS2 False String MACS2 Name scATAC-seq Level 2,scATAC-seq Level 3 Name of the peak in MACS2 False String MACS2 Score scATAC-seq Level 2,scATAC-seq Level 3 Peak score (proportional to q-value) in MACS2 False String MACS2 Fold Change scATAC-seq Level 2,scATAC-seq Level 3 Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2 False String MACS2 Neg Log10 pvalue Summit scATAC-seq Level 2,scATAC-seq Level 3 Negative log10 p-value for the peak summit in MACS2 False String MACS2 Neg Log10 qvalue Summit scATAC-seq Level 2,scATAC-seq Level 3 Negative log10 q-value for the peak summit in MACS2 False String MACS2 Relative Summit Position scATAC-seq Level 2,scATAC-seq Level 3 Position of the peak summit related to the start position in MACS2 False String scATAC-seq Object ID scATAC-seq Level 3 Orig.Ident or scATAC-seq Object ID False String scATACseq Workflow Type scATAC-seq Level 4 Generic name for the workflow used to analyze a data set. True String scATACseq Workflow Parameters Description scATAC-seq Level 4 Parameters used to run the scATAC-seq workflow. True String scmCseq Read1 scmC-seq Level 1 Read 1 content description True String Cell Barcode and UMI cDNA scmCseq Read2 scmC-seq Level 1 Read 2 content description True String Cell Barcode and UMI cDNA scmCseq Read3 scmC-seq Level 1 Read 3 content description True String Cell Barcode and UMI cDNA Single Nucleus Capture scmC-seq Level 1 Nuclei isolation method False String Plates 10x droplet Bisulfite Conversion scmC-seq Level 1,Bulk Methylation-seq Level 1 Name of the kit used in bisulfite conversion. True String Zimo EZ DNA Methylation Kit Zimo EZ-96 DNA Methylation Shallow Kit Zimo EZ-96 DNA Methylation Deep Kit NEBNext Enzymatic Methyl-seq Kit Agilent SureSelectXT Methyl-Seq Target Capture Kit Bulk WES Level 1 Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version. True String Not Applicable Custom Targets File Provided Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes Custom GENIE-DFCI OncoPanel - 275 Genes Custom GENIE-DFCI Oncopanel - 300 Genes Custom GENIE-DFCI Oncopanel - 447 Genes Custom HaloPlex DLBCL Panel - 370 Genes Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes Custom Large Construct Capture TARGET-OS Panel - 8 Genes Custom MSK IMPACT Panel - 341 Genes Custom MSK IMPACT Panel - 410 Genes Custom MSK IMPACT Panel - 468 Genes Custom Myeloid GENIE-VICC Panel - 37 Genes Custom Personalis ACEcp VAREPOP-APOLLO Panel v2 Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1 Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2 Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb Custom Solid Tumor GENIE-VICC Panel - 34 Genes Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb Custom SureSelect GENIE-UHN Panel - 555 Genes Custom SureSelect Human All Exon v1.1 Plus 3 Boosters Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb Custom Twist Broad Exome v1.0 - 35.0 Mb Custom Twist Broad PanCancer Panel - 396 Genes Foundation Medicine T5a Panel - 322 Genes Foundation Medicine T7 Panel - 429 Genes Ion AmpliSeq Cancer Hotspot Panel v2 Ion AmpliSeq Comprehensive Cancer Panel Nextera DNA Exome Nextera Rapid Capture Exome v1.2 SeqCap EZ HGSC VCRome v2.1 SeqCap EZ Human Exome v2.0 SeqCap EZ Human Exome v3.0 SureSelect Human All Exon v3 SureSelect Human All Exon v4 SureSelect Human All Exon v5 SureSelect Human All Exon v5 + UTR TruSeq Amplicon Cancer Panel TruSeq Exome Enrichment - 62 Mb TruSeq RNA Exome TruSight Myeloid Sequencing Panel xGen Exome Research Panel v1.0 xGen Universal Blocking Oligo – TS HT-i5 - 25 rxn 25 rxn xGen Universal Blocking Oligo – TS HT-i7 SureSelect Human All Exon v6 unknown MSI Workflow Link Bulk WES Level 2,Bulk RNA-seq Level 2 Link to method workflow (or command) used in estimating the MSI. URL False String MSI Score Bulk WES Level 2,Bulk RNA-seq Level 2 Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number False String MSI Status Bulk WES Level 2,Bulk RNA-seq Level 2 MSIsensor determination of either microsatellite stability or instability. False String MSI MSI-low MSI-high MSS Germline Variants Workflow URL Bulk WES Level 3 Link to workflow document, e.g. Github, DockStore.org recommended True String Germline Variants Workflow Type Bulk WES Level 3 Generic name for the workflow used to analyze a data set False String GATK4 Other Germline Variants Workflow Type None Somatic Variants Workflow URL Bulk WES Level 3 Generic name for the workflow used to analyze a data set. True String Somatic Variants Workflow Type Bulk WES Level 3 Generic name for the workflow used to analyze a data set. False String CaVEMan GATK4 MuTect2 MuSE Pindel SomaticSniper VarScan2 Other Somatic Variants Workflow Type None Somatic Variants Sample Type Bulk WES Level 3 Is the sample case or control in somatic variant analysis True String Case Sample Control Sample Not Applicable Structural Variant Workflow URL Bulk WES Level 3 Link to workflow document. DockStore.org recommended. URL True String Structural Variant Workflow Type Bulk WES Level 3 Generic name for the workflow used to analyze a data set. False String BRASS GATK4 CNV CNVkit Other Structural Variant Workflow Type None Replicate Type Bulk Methylation-seq Level 1 A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples. True String Technical replicate Biological replicate Not Applicable Bulk Methylation Assay Type Bulk Methylation-seq Level 1 Assay types normally determine genomic coverage True String Whole genome Targeted Genome Beadchip Array Total DNA Input Bulk Methylation-seq Level 1 Overall number of reads for a given sample in digits (microgram, nanogram). False String Trimmer Bulk Methylation-seq Level 2 Software used for trimming True String FASTX toolkit SolexaQA Btrim Cutadapt Kraken PRINSEQ Adapter removal Trim Galore! ConDeTri ERNE-FILTER Trimmo-matic Bulk Methylation Genomic Reference Bulk Methylation-seq Level 2 The human genome reference used in the alignment of reads True String HG19 HG38 T2T CHM13 Duplicate Removal Software Bulk Methylation-seq Level 2 Software used for remove duplicate reads True String Samtools sort picard MarkDuplicates Proportion of Minimum CpG Coverage 10X Bulk Methylation-seq Level 2 Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG. False String DMC Calling Tool Bulk Methylation-seq Level 3 Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR) True String MethylKit BSmooth BiSeq MethylSig DSS MOABS DSS-single metilene MACAU MethylDackel DMC Calling Workflow URL Bulk Methylation-seq Level 3 Generic name for the workflow used to analyze a data set True String DMR Calling Tool Bulk Methylation-seq Level 3 Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR) True String MethylKit BSmooth BiSeq MethylSig DSS MOABS DSS-single metilene MACAU DMR Calling Workflow URL Bulk Methylation-seq Level 3 Generic name for the workflow used to analyze a data set True String pUC19 methylation ratio Bulk Methylation-seq Level 3 Methylation ratio of mostly methylated pUC19 control, as a percentage True String Lambda methylation ratio Bulk Methylation-seq Level 3 Methylation ratio of mostly unmethylated lambda control, as a percentage True String DMC data file format Bulk Methylation-seq Level 3 Format of the data files True String BED bedGraph DMR data file Format Bulk Methylation-seq Level 3 Format of the data files. True String BED bedGraph Micro-region Seq Platform Bulk RNA-seq Level 1 The platform used for micro-regional RNA sequencing (if applicable) False String Rarecyte Pick-Seq Laser Capture Microdissection ROI Tag Bulk RNA-seq Level 1 The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3. False String Transcript Integrity Number Bulk RNA-seq Level 1 Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number False String RIN Bulk RNA-seq Level 1 A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number False String DV200 Bulk RNA-seq Level 1 Represents the percentage of RNA fragments that are >200 nucleotides in size. Number False String Pseudo Alignment Used Bulk RNA-seq Level 3 Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used. True String Yes - Pseudo Alignment Used no Expression Units Bulk RNA-seq Level 3 How quantities are corrected for gene length True String TPM RPKM FPKM Counts Other NA Fusion Gene Detected Bulk RNA-seq Level 3 Was a fusion gene identified? False String Yes - Fusion Gene Detected no unknown Fusion Gene Identity Bulk RNA-seq Level 3 The gene symbols of fused genes. False String EWS-FLI EWS-ERG SYT-SSX1 SYT-SSX2 EWS-WT1 Other Fusion Gene Crosslinking Condtion HI-C-seq Level 1 Detailed condition for DNA crosslinking True String DNA Digestion Condition HI-C-seq Level 1 Enzymes and treatment length/temperature for genome digestion True String Nuclei Permeabilization Method HI-C-seq Level 1 Detergent and treatment condition for nuclei permeabilization and crosslinking softening True String Ligation Condition HI-C-seq Level 1 Name of ligase and condition for proximity ligation True String Biotin Enrichment HI-C-seq Level 1 Whether biotin is used for enriching ligation product True String yes no DNA Input Amount HI-C-seq Level 1 Amount of DNA for library construction, in nanograms. True String Aligned Read Length HI-C-seq Level 2,scRNA-seq Level 2 Read length used for alignment if hard trimming was applied True Applied Hard Trimming is "Yes - Applied Hard Trimming" String Tool HI-C-seq Level 2 Were any software or computational tools generated for this content True String yes no Resolution HI-C-seq Level 2 Binning size used for generating contact matrix, in basepair. True String Normalization Method HI-C-seq Level 2 Description of Normalization Process False String Stripe Calling HI-C-seq Level 3 Tool used for identifying architectural stripe-forming, interaction hotspots. True String MACS2 Other Loop Window HI-C-seq Level 3 Binning size used for calling significant dot interactions (loops) True String Stripe Window HI-C-seq Level 3 Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different. True String Loop Calling HI-C-seq Level 3 Tool used for identifying loop interactions True String HiCCUPS Cooltools Other cDNA scRNA-seq Level 1,scmC-seq Level 1 Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase False String ERCC scRNA-seq Level 1 The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization False String Yes - Applied Hard Trimming scRNA-seq Level 2 Hard Trimming was applied False String Yes - Trim Adapter Sequence scDNA-seq Level 1 Trim adapter sequence False String Adapter Trimmer Name Adapter Trimmer Version Adapter Trimmer Options Other Alignment Workflow scDNA-seq Level 2 Other Alignment Workflow False String Other Germline Variants Workflow Type Bulk WES Level 3 Other Germline Variants Workflow Type False String Other Somatic Variants Workflow Type Bulk WES Level 3 Other Somatic Variants Workflow Type False String Other Structural Variant Workflow Type Bulk WES Level 3 Other Structural Variant Workflow Type False String Targeted Genome Bulk Methylation-seq Level 1 Assay for analyzing specific mutations in a given sample False String MeDIP RRBS Beadchip Array Bulk Methylation-seq Level 1 Assay that uses beads to target a specific locus on the genome. False String HM27K HM450K Yes - Pseudo Alignment Used Bulk RNA-seq Level 3 Pseudo aligner was used False String Yes - Fusion Gene Detected Bulk RNA-seq Level 3 A fusion gene was detected False String Other Fusion Gene Bulk RNA-seq Level 3 Other fusion gene detected. False String cDNA Offset scRNA-seq Level 1 Offset in sequence for cDNA read (in bp): number True Spatial Read2 is "cDNA" String cDNA Length scRNA-seq Level 1 Length of cDNA read (in bp): number True Spatial Read2 is "cDNA" String Spike In Concentration scRNA-seq Level 1 The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910] True Spike In is "ERCC" String Adapter Trimmer Name scDNA-seq Level 1 Name of adapter trimmer False String Adapter Trimmer Version scDNA-seq Level 1 Version of the adapter trimmer False String Adapter Trimmer Options scDNA-seq Level 1 Options used by adapter trimmer False String Custom Alignment Workflow scDNA-seq Level 2 Specify the name of a custom alignment workflow True Alignment is "Other Alignment Workflow" String Custom Germline Variants Workflow Type Bulk WES Level 3 Specify the name of a custom alignment workflow True Germline is "Other" String Custom Somatic Variants Workflow Type Bulk WES Level 3 Specify the name of a custom workflow name True Somatic is "Other" String Custom Structural Variant Workflow Type Bulk WES Level 3 Specify the name of a custom workflow name True Structural is "Other" String Software and Version Bulk RNA-seq Level 3 Name of software used to generate expression values. String True Pseudo Alignment Used is "Yes - Pseudo Alignment Used" String Specify Other Fusion Gene Bulk RNA-seq Level 3 Specify fusion gene detected, if not in list False Fusion Gene Identity is "Other Fusion Gene" String