Resource
| Id | DNase-seq/ENCSR139PLJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR139PLJ [biosample_summary="Homo sapiens activated CD4-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 50 U/mL Interleukin-2 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, 50 U/mL Interleukin-2 for 1 hour output_type: peaks audit_warning: Alignment file {ENCFF783MHU|/files/ENCFF783MHU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 48313964 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 {ENCFF783MHU|/files/ENCFF783MHU/} 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_ENCSR139PLJ | float |
DNase-seq_ENCSR139PLJ |
DNase-seq ENCSR139PLJ [biosample_summary="Homo sapiens activated CD4-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 50 U/mL Interleukin-2 for 1 hour"]
|
 |
[0.27, 29] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4957945 | 0.15% | 25099 |
| chr1 | 518644 | 0.21% | 2645 |
| chr2 | 329800 | 0.14% | 1669 |
| chr3 | 263134 | 0.13% | 1328 |
| chr4 | 163601 | 0.09% | 823 |
| chr5 | 210839 | 0.12% | 1062 |
| chr6 | 274049 | 0.16% | 1388 |
| chr7 | 221030 | 0.14% | 1124 |
| chr8 | 168377 | 0.12% | 873 |
| chr9 | 196263 | 0.14% | 1007 |
| chr10 | 206855 | 0.15% | 1066 |
| chr11 | 260095 | 0.19% | 1336 |
| chr12 | 264809 | 0.20% | 1308 |
| chr13 | 94292 | 0.08% | 466 |
| chr14 | 173706 | 0.16% | 888 |
| chr15 | 159050 | 0.16% | 821 |
| chr16 | 215484 | 0.24% | 1084 |
| chr17 | 317084 | 0.38% | 1622 |
| chr18 | 68356 | 0.09% | 345 |
| chr19 | 393844 | 0.67% | 1906 |
| chr20 | 136146 | 0.21% | 703 |
| chr21 | 55201 | 0.12% | 280 |
| chr22 | 125159 | 0.25% | 635 |
| chrX | 136666 | 0.09% | 693 |
| chrY | 5461 | 0.01% | 27 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 25099 | 7 | 842 | 197.54 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF341QVB.bed.gz | 278.21 KB | d357aaa0d9493356b7ed0d71d2390d4e |
| ENCFF341QVB.tabix.bed.gz | 252.87 KB | 8204173023aec60f51d55568628325b6 |
| ENCFF341QVB.tabix.bed.gz.tbi | 148.65 KB | a03630bff59778e05212559beb0324e9 |
| genomic_resource.yaml | 3.2 KB | 003e8720226b58b5530e58e7b993e0a5 |
| statistics/ |