Resource
| Id | DNase-seq/ENCSR133OSO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR133OSO [biosample_summary="Homo sapiens activated CD4-positive, CD25-positive, alpha-beta regulatory T cell male adult (38 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 (38 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 {ENCFF139SFY|/files/ENCFF139SFY/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 42507818 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 {ENCFF139SFY|/files/ENCFF139SFY/} 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_ENCSR133OSO | float |
DNase-seq_ENCSR133OSO |
DNase-seq ENCSR133OSO [biosample_summary="Homo sapiens activated CD4-positive, CD25-positive, alpha-beta regulatory T cell male adult (38 years) treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours"]
|
 |
[0.331, 34.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6102180 | 0.19% | 32905 |
| chr1 | 622785 | 0.25% | 3362 |
| chr2 | 415825 | 0.17% | 2264 |
| chr3 | 333830 | 0.17% | 1825 |
| chr4 | 205013 | 0.11% | 1101 |
| chr5 | 266104 | 0.15% | 1434 |
| chr6 | 356385 | 0.21% | 1926 |
| chr7 | 282159 | 0.18% | 1532 |
| chr8 | 218762 | 0.15% | 1187 |
| chr9 | 233060 | 0.17% | 1250 |
| chr10 | 264566 | 0.20% | 1431 |
| chr11 | 313351 | 0.23% | 1692 |
| chr12 | 322677 | 0.24% | 1719 |
| chr13 | 120419 | 0.11% | 641 |
| chr14 | 219112 | 0.20% | 1184 |
| chr15 | 201854 | 0.20% | 1088 |
| chr16 | 261602 | 0.29% | 1410 |
| chr17 | 373656 | 0.45% | 2018 |
| chr18 | 87653 | 0.11% | 491 |
| chr19 | 440760 | 0.75% | 2293 |
| chr20 | 167734 | 0.26% | 930 |
| chr21 | 66394 | 0.14% | 358 |
| chr22 | 148428 | 0.29% | 807 |
| chrX | 173293 | 0.11% | 927 |
| chrY | 6758 | 0.01% | 35 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 32905 | 3 | 940 | 185.45 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF875KTF.bed.gz | 362.91 KB | 58832492901218741a75d09891d2cffb |
| ENCFF875KTF.tabix.bed.gz | 328.57 KB | bdbd203a41c4eaaf3652ef3de8f2d9c7 |
| ENCFF875KTF.tabix.bed.gz.tbi | 182.83 KB | 3a565662abfdf56c117a51bf71a1105c |
| genomic_resource.yaml | 3.47 KB | b8b07d8b92521be89e5f1ec59fa3dc8d |
| statistics/ |