Resource
| Id | DNase-seq/ENCSR050VTC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR050VTC [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 24 hours, 100 ng/mL Interleukin-23 for 24 hours, 100 ng/mL Interleukin-1b for 24 hours"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL Interleukin-23 for 24 hours, 100 ng/mL Interleukin-1b for 24 hours output_type: peaks audit_warning: Alignment file {ENCFF423FCI|/files/ENCFF423FCI/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 22668540 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 {ENCFF423FCI|/files/ENCFF423FCI/} 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_ENCSR050VTC | float |
DNase-seq_ENCSR050VTC |
DNase-seq ENCSR050VTC [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 24 hours, 100 ng/mL Interleukin-23 for 24 hours, 100 ng/mL Interleukin-1b for 24 hours"]
|
 |
[0.443, 21.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5192582 | 0.16% | 28514 |
| chr1 | 539646 | 0.22% | 2963 |
| chr2 | 359300 | 0.15% | 1970 |
| chr3 | 280093 | 0.14% | 1546 |
| chr4 | 189671 | 0.10% | 1035 |
| chr5 | 232210 | 0.13% | 1294 |
| chr6 | 291893 | 0.17% | 1627 |
| chr7 | 244869 | 0.15% | 1341 |
| chr8 | 184013 | 0.13% | 1021 |
| chr9 | 210235 | 0.15% | 1165 |
| chr10 | 220225 | 0.16% | 1228 |
| chr11 | 278073 | 0.21% | 1537 |
| chr12 | 268320 | 0.20% | 1465 |
| chr13 | 112835 | 0.10% | 592 |
| chr14 | 176894 | 0.17% | 966 |
| chr15 | 166824 | 0.16% | 928 |
| chr16 | 221256 | 0.24% | 1201 |
| chr17 | 298762 | 0.36% | 1625 |
| chr18 | 80531 | 0.10% | 446 |
| chr19 | 372204 | 0.63% | 1986 |
| chr20 | 142320 | 0.22% | 798 |
| chr21 | 57931 | 0.12% | 331 |
| chr22 | 131070 | 0.26% | 713 |
| chrX | 128954 | 0.08% | 710 |
| chrY | 4453 | 0.01% | 26 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 28514 | 2 | 820 | 182.11 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF817BLK.bed.gz | 304.02 KB | e5421e57bfbd6bb7f9b4b2542591eedb |
| ENCFF817BLK.tabix.bed.gz | 273.62 KB | 0b667873faad9698835c441d5af5f952 |
| ENCFF817BLK.tabix.bed.gz.tbi | 168.29 KB | 230fbf1452c913e7856e0d780d43b82f |
| genomic_resource.yaml | 3.47 KB | 5277e15da6e76c8426c3c6fde5901f83 |
| statistics/ |