Resource
| Id | DNase-seq/ENCSR724QTW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR724QTW [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 4 hours, 100 ng/mL Interleukin-12 subunit alpha for 4 hours, 100 ng/mL Interleukin-12 subunit beta for 4 hours"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-12 subunit alpha for 4 hours, 100 ng/mL Interleukin-12 subunit beta for 4 hours output_type: peaks audit_warning: Alignment file {ENCFF482JGP|/files/ENCFF482JGP/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 28190626 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 {ENCFF482JGP|/files/ENCFF482JGP/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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_ENCSR724QTW | float |
DNase-seq_ENCSR724QTW |
DNase-seq ENCSR724QTW [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 4 hours, 100 ng/mL Interleukin-12 subunit alpha for 4 hours, 100 ng/mL Interleukin-12 subunit beta for 4 hours"]
|
 |
[0.427, 25.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5566980 | 0.17% | 30902 |
| chr1 | 571864 | 0.23% | 3174 |
| chr2 | 390432 | 0.16% | 2183 |
| chr3 | 307161 | 0.15% | 1720 |
| chr4 | 196157 | 0.10% | 1081 |
| chr5 | 244510 | 0.13% | 1384 |
| chr6 | 324112 | 0.19% | 1802 |
| chr7 | 252236 | 0.16% | 1407 |
| chr8 | 204452 | 0.14% | 1163 |
| chr9 | 215960 | 0.16% | 1211 |
| chr10 | 237996 | 0.18% | 1339 |
| chr11 | 297946 | 0.22% | 1641 |
| chr12 | 302927 | 0.23% | 1646 |
| chr13 | 111776 | 0.10% | 611 |
| chr14 | 192739 | 0.18% | 1072 |
| chr15 | 179320 | 0.18% | 1012 |
| chr16 | 232535 | 0.26% | 1269 |
| chr17 | 332651 | 0.40% | 1864 |
| chr18 | 83528 | 0.10% | 467 |
| chr19 | 396763 | 0.68% | 2101 |
| chr20 | 149657 | 0.23% | 856 |
| chr21 | 62469 | 0.13% | 359 |
| chr22 | 135194 | 0.27% | 740 |
| chrX | 139442 | 0.09% | 771 |
| chrY | 5153 | 0.01% | 29 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 30902 | 20 | 700 | 180.15 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF462CWQ.bed.gz | 334.25 KB | 99d6b8d8fb82ba8427b455840e2ff3a7 |
| ENCFF462CWQ.tabix.bed.gz | 299.87 KB | 02e37986bd88c38fe691d43d04c4054e |
| ENCFF462CWQ.tabix.bed.gz.tbi | 182.64 KB | b37e268817498c2f17961570f14b9425 |
| genomic_resource.yaml | 3.59 KB | 92c047c1d31c7c8ee3b71406927a289f |
| statistics/ |