Resource
| Id | DNase-seq/ENCSR442SDV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR442SDV [biosample_summary="Homo sapiens activated CD8-positive, alpha-beta memory T cell female adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 48 hours"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 48 hours output_type: peaks audit_warning: Alignment file {ENCFF398QOP|/files/ENCFF398QOP/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 48832594 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 {ENCFF398QOP|/files/ENCFF398QOP/} 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_ENCSR442SDV | float |
DNase-seq_ENCSR442SDV |
DNase-seq ENCSR442SDV [biosample_summary="Homo sapiens activated CD8-positive, alpha-beta memory T cell female adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 48 hours"]
|
 |
[0.226, 11.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7232677 | 0.22% | 31592 |
| chr1 | 731543 | 0.29% | 3158 |
| chr2 | 508701 | 0.21% | 2205 |
| chr3 | 411821 | 0.21% | 1735 |
| chr4 | 277733 | 0.15% | 1176 |
| chr5 | 321926 | 0.18% | 1361 |
| chr6 | 421828 | 0.25% | 1822 |
| chr7 | 341601 | 0.21% | 1485 |
| chr8 | 254980 | 0.18% | 1150 |
| chr9 | 292688 | 0.21% | 1275 |
| chr10 | 308662 | 0.23% | 1361 |
| chr11 | 380223 | 0.28% | 1668 |
| chr12 | 395895 | 0.30% | 1689 |
| chr13 | 145007 | 0.13% | 621 |
| chr14 | 247541 | 0.23% | 1082 |
| chr15 | 236916 | 0.23% | 1039 |
| chr16 | 303991 | 0.34% | 1358 |
| chr17 | 427615 | 0.51% | 1872 |
| chr18 | 114252 | 0.14% | 513 |
| chr19 | 488842 | 0.83% | 2148 |
| chr20 | 188278 | 0.29% | 886 |
| chr21 | 78813 | 0.17% | 361 |
| chr22 | 169284 | 0.33% | 780 |
| chrX | 184537 | 0.12% | 847 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 31592 | 1 | 1140 | 228.94 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF810ZJY.bed.gz | 326.56 KB | d0fa1cc1db1d358fa5c2f1bddbd46400 |
| ENCFF810ZJY.tabix.bed.gz | 304.06 KB | 894bd8001db508ae79e9387cb2dbe474 |
| ENCFF810ZJY.tabix.bed.gz.tbi | 163.83 KB | aeeec3d1812ee5110c1b0d7e654f5e6f |
| genomic_resource.yaml | 3.08 KB | 67727e382567585ee0c4deed1b8648aa |
| statistics/ |