Other (26)
- ANALYTE_TYPE - Analyte Type (phv00543195.v1.p1)
- BODY_SITE - Body site where sample was collected (phv00543194.v1.p1)
- FILE_ID - ID of the fastq files (phv00543202.v1.p1)
- HISTOLOGICAL_TYPE - Cell or tissue type or subtype of sample (phv00543197.v1.p1)
- IS_INCLUDED_IN_MANUSCRIPT - Whether the library was included in the final set used for analyses in PMID: 34699533 (Perrin and Currin et al. 2021) (phv00543218.v1.p1)
- IS_TUMOR - Tumor status (phv00543196.v1.p1)
- LAB - Lab in which the ATAC-seq experiments were performed (phv00543203.v1.p1)
- NUM_AFTER_DUPS_REMOVED - Number of nuclear alignments after removing duplicates (phv00543212.v1.p1)
- NUM_CHR_M - Number of reads aligning to the mitochondrial chromosome (phv00543210.v1.p1)
- NUM_FILTERED - Number of adapter-trimmed and base quality-trimmed ATAC reads before alignment (phv00543206.v1.p1)
- NUM_N_PEAKS - Number of narrow peaks called by MACS2 (phv00543214.v1.p1)
- NUM_NUCLEAR - Number of reads aligned to nuclear chromosomes (chr1-22, X, Y) (phv00543208.v1.p1)
- NUM_RAW - Number of raw ATAC sequenced reads (phv00543205.v1.p1)
- NUM_UNIQUE_ALIGNED - Number of reads aligned to the hg19 genome with mapq>20 (phv00543207.v1.p1)
- PERCENT_AFTER_DUPS_REMOVED - Percentage of nuclear reads remaining after duplicate removal (phv00543213.v1.p1)
- PERCENT_CHR_M - Percentage of uniquely aligned reads mapping to the mitochondrial chromosome (phv00543211.v1.p1)
- PERCENT_NUCLEAR - Percentage of uniquely aligned reads on nuclear chromosomes (phv00543209.v1.p1)
- PERCENT_READS_IN_N_PEAKS - Percentage of non-duplicated, nuclear alignments overlapping narrow peaks (phv00543215.v1.p1)
- PROTOCOL - Version of the ATAC-seq protocol used (phv00543198.v1.p1)
- READ_LENGTH - Read length; many samples were trimmed to 50nt for consistent read length (phv00543204.v1.p1)
- READ_TYPE - Indicates if single- or paired-end sequencing (phv00543201.v1.p1)
- SAMPLE_ID - Sample ID (phv00543193.v1.p1)
- TISSUE_AMOUNT - Amount of adipose tissue used, either in milligrams or number of cells depending on the protocol (phv00543199.v1.p1)
- TN5_CONCENTRATION - Amount of the Tn5 transposase used in the ATAC-seq protocol (phv00543200.v1.p1)
- TSS_ENRICHMENT_ATAQV - TSS enrichment calculated by ataqv (phv00543216.v1.p1)
- TSS_ENRICHMENT_MYSCRIPT - TSS enrichment calculated by a customized script that allows single-end libraries (phv00543217.v1.p1)