Resource
| Id | DNase-seq/ENCSR618HFT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR618HFT [biosample_summary="Homo sapiens stimulated activated CD4-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL TNF-alpha for 1 hour"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL TNF-alpha for 1 hour output_type: peaks audit_warning: Alignment file {ENCFF159XDU|/files/ENCFF159XDU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 21661012 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 {ENCFF159XDU|/files/ENCFF159XDU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR618HFT | float |
DNase-seq_ENCSR618HFT |
DNase-seq ENCSR618HFT [biosample_summary="Homo sapiens stimulated activated CD4-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL TNF-alpha for 1 hour"]
|
 |
[0.371, 52.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4528472 | 0.14% | 25247 |
| chr1 | 471818 | 0.19% | 2632 |
| chr2 | 305700 | 0.13% | 1705 |
| chr3 | 240389 | 0.12% | 1363 |
| chr4 | 146034 | 0.08% | 805 |
| chr5 | 193827 | 0.11% | 1087 |
| chr6 | 248538 | 0.15% | 1401 |
| chr7 | 207952 | 0.13% | 1161 |
| chr8 | 157126 | 0.11% | 885 |
| chr9 | 184223 | 0.13% | 1027 |
| chr10 | 183530 | 0.14% | 1049 |
| chr11 | 240282 | 0.18% | 1328 |
| chr12 | 239550 | 0.18% | 1324 |
| chr13 | 84490 | 0.07% | 470 |
| chr14 | 156817 | 0.15% | 875 |
| chr15 | 141382 | 0.14% | 797 |
| chr16 | 200410 | 0.22% | 1113 |
| chr17 | 295565 | 0.36% | 1676 |
| chr18 | 63226 | 0.08% | 352 |
| chr19 | 353378 | 0.60% | 1879 |
| chr20 | 123686 | 0.19% | 720 |
| chr21 | 53100 | 0.11% | 296 |
| chr22 | 115454 | 0.23% | 642 |
| chrX | 116741 | 0.07% | 630 |
| chrY | 5254 | 0.01% | 30 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 25247 | 6 | 740 | 179.37 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF992ZCX.bed.gz | 276.8 KB | 3db7e01483f447fb35b1d29d65709d99 |
| ENCFF992ZCX.tabix.bed.gz | 248.08 KB | 38b837576f5b4e5fd72406831fc015f4 |
| ENCFF992ZCX.tabix.bed.gz.tbi | 154.36 KB | 590aa05377976295be7e9677dde00512 |
| genomic_resource.yaml | 3.22 KB | f3639b68d43f44489cf38de1c0528cfd |
| statistics/ |