Resource
| Id | DNase-seq/ENCSR933VOY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR933VOY [biosample_summary="Homo sapiens activated CD8-positive, alpha-beta memory T cell male adult (38 years) treated with anti-CD3 and anti-CD28 coated beads for 24 hours"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (38 years) treated with anti-CD3 and anti-CD28 coated beads for 24 hours output_type: peaks audit_warning: Alignment file {ENCFF835QKX|/files/ENCFF835QKX/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 48520876 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) audit_warning: Signal Portion of Tags (SPOT) is a measure of enrichment, analogous to the commonly used fraction of reads in peaks metric. ENCODE processed alignment files {ENCFF835QKX|/files/ENCFF835QKX/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.36. According to ENCODE standards, SPOT1 score of 0.4 or higher is considered a product of high quality data. Any sample with a SPOT1 score <0.3 should be targeted for replacement with a higher quality sample, and a SPOT1 score of 0.25 is considered minimally acceptable SPOT1 score of 0.25 is considered minimally acceptable for rare and hard to find primary tissues. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR933VOY | float |
DNase-seq_ENCSR933VOY |
DNase-seq ENCSR933VOY [biosample_summary="Homo sapiens activated CD8-positive, alpha-beta memory T cell male adult (38 years) treated with anti-CD3 and anti-CD28 coated beads for 24 hours"]
|
 |
[0.289, 17.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6398854 | 0.20% | 32715 |
| chr1 | 652403 | 0.26% | 3338 |
| chr2 | 430939 | 0.18% | 2198 |
| chr3 | 360796 | 0.18% | 1806 |
| chr4 | 233757 | 0.12% | 1149 |
| chr5 | 286701 | 0.16% | 1457 |
| chr6 | 363798 | 0.21% | 1869 |
| chr7 | 295204 | 0.19% | 1525 |
| chr8 | 227068 | 0.16% | 1183 |
| chr9 | 256254 | 0.19% | 1328 |
| chr10 | 272877 | 0.20% | 1410 |
| chr11 | 332200 | 0.25% | 1705 |
| chr12 | 334905 | 0.25% | 1711 |
| chr13 | 127044 | 0.11% | 627 |
| chr14 | 223422 | 0.21% | 1161 |
| chr15 | 208271 | 0.20% | 1077 |
| chr16 | 271901 | 0.30% | 1393 |
| chr17 | 388121 | 0.47% | 1981 |
| chr18 | 95763 | 0.12% | 493 |
| chr19 | 472619 | 0.81% | 2332 |
| chr20 | 171406 | 0.27% | 923 |
| chr21 | 69591 | 0.15% | 364 |
| chr22 | 151677 | 0.30% | 801 |
| chrX | 167102 | 0.11% | 858 |
| chrY | 5035 | 0.01% | 26 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 32715 | 7 | 840 | 195.59 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF401WTQ.bed.gz | 354.29 KB | d57f1690cb836ec449955df04fa1a6eb |
| ENCFF401WTQ.tabix.bed.gz | 322.94 KB | b5e2f81dc5ec62112451fb7e876d6a97 |
| ENCFF401WTQ.tabix.bed.gz.tbi | 177.08 KB | c0ba1b50823ab2c665c66936d02d2832 |
| genomic_resource.yaml | 3.07 KB | 45c71ae1f8c1ee06df9a85b4a6ca7bc1 |
| statistics/ |