Resource
| Id | DNase-seq/ENCSR044JIR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR044JIR [biosample_summary="Homo sapiens activated naive CD8-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours output_type: peaks audit_warning: Alignment file {ENCFF187TZE|/files/ENCFF187TZE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 40054438 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 {ENCFF187TZE|/files/ENCFF187TZE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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_ENCSR044JIR | float |
DNase-seq_ENCSR044JIR |
DNase-seq ENCSR044JIR [biosample_summary="Homo sapiens activated naive CD8-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours"]
|
 |
[0.251, 25.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5587198 | 0.17% | 31083 |
| chr1 | 585229 | 0.24% | 3244 |
| chr2 | 386424 | 0.16% | 2164 |
| chr3 | 298833 | 0.15% | 1666 |
| chr4 | 188638 | 0.10% | 1038 |
| chr5 | 240003 | 0.13% | 1353 |
| chr6 | 324489 | 0.19% | 1820 |
| chr7 | 251043 | 0.16% | 1405 |
| chr8 | 198978 | 0.14% | 1133 |
| chr9 | 219352 | 0.16% | 1218 |
| chr10 | 227604 | 0.17% | 1274 |
| chr11 | 287457 | 0.21% | 1598 |
| chr12 | 291975 | 0.22% | 1633 |
| chr13 | 104665 | 0.09% | 590 |
| chr14 | 200427 | 0.19% | 1124 |
| chr15 | 177232 | 0.17% | 999 |
| chr16 | 238752 | 0.26% | 1309 |
| chr17 | 347410 | 0.42% | 1921 |
| chr18 | 80968 | 0.10% | 455 |
| chr19 | 421398 | 0.72% | 2252 |
| chr20 | 155117 | 0.24% | 896 |
| chr21 | 63786 | 0.14% | 349 |
| chr22 | 138957 | 0.27% | 772 |
| chrX | 153125 | 0.10% | 842 |
| chrY | 5336 | 0.01% | 28 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 31083 | 5 | 720 | 179.75 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF459UHN.bed.gz | 340.22 KB | 0bb2777d9f45763916c5c44bbabd450e |
| ENCFF459UHN.tabix.bed.gz | 307.99 KB | 61be49f3b869506ff83e2fb844a43434 |
| ENCFF459UHN.tabix.bed.gz.tbi | 175.6 KB | 5b4ecbda56c2672a7c62868441ed7c9e |
| genomic_resource.yaml | 3.46 KB | 71a50bc51173f81266da9bbe0eb1df6d |
| statistics/ |