Resource
| Id | DNase-seq/ENCSR210JVF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR210JVF [biosample_summary="Homo sapiens stimulated activated CD8-positive, alpha-beta memory T cell female adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL Interleukin-4 for 1 hour"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL Interleukin-4 for 1 hour output_type: peaks audit_warning: Alignment file {ENCFF393MQG|/files/ENCFF393MQG/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 28419080 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 {ENCFF393MQG|/files/ENCFF393MQG/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR210JVF | float |
DNase-seq_ENCSR210JVF |
DNase-seq ENCSR210JVF [biosample_summary="Homo sapiens stimulated activated CD8-positive, alpha-beta memory T cell female adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL Interleukin-4 for 1 hour"]
|
 |
[0.496, 23.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4968514 | 0.15% | 26085 |
| chr1 | 516359 | 0.21% | 2694 |
| chr2 | 345710 | 0.14% | 1834 |
| chr3 | 274124 | 0.14% | 1416 |
| chr4 | 168351 | 0.09% | 866 |
| chr5 | 217311 | 0.12% | 1135 |
| chr6 | 279224 | 0.16% | 1462 |
| chr7 | 236336 | 0.15% | 1232 |
| chr8 | 171086 | 0.12% | 921 |
| chr9 | 201723 | 0.15% | 1060 |
| chr10 | 203096 | 0.15% | 1092 |
| chr11 | 259459 | 0.19% | 1363 |
| chr12 | 253924 | 0.19% | 1310 |
| chr13 | 100233 | 0.09% | 517 |
| chr14 | 175375 | 0.16% | 930 |
| chr15 | 162522 | 0.16% | 852 |
| chr16 | 215773 | 0.24% | 1140 |
| chr17 | 309550 | 0.37% | 1642 |
| chr18 | 72178 | 0.09% | 386 |
| chr19 | 367772 | 0.63% | 1881 |
| chr20 | 133631 | 0.21% | 731 |
| chr21 | 53866 | 0.12% | 289 |
| chr22 | 115902 | 0.23% | 632 |
| chrX | 135009 | 0.09% | 700 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 26085 | 1 | 760 | 190.47 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF083CXT.bed.gz | 279.45 KB | 117d2c89d2773f7598dba94ad25e3b40 |
| ENCFF083CXT.tabix.bed.gz | 252.82 KB | a90b32c7499eb63ac318ed0b7989cb64 |
| ENCFF083CXT.tabix.bed.gz.tbi | 151.96 KB | 240a455db8f381033bb9c7e0f35aab3a |
| genomic_resource.yaml | 3.27 KB | 32c1efce25122edb32030ec42f25e28e |
| statistics/ |