Resource
| Id | DNase-seq/ENCSR636DIR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR636DIR [biosample_summary="Homo sapiens activated T-helper 1 cell\ \ male adult (35 years) treated with anti-CD3 and anti-CD28 coated beads for 24\ \ hours, 30 ng/mL Interleukin-12 subunit beta for 36 hours, 10 ng/mL Interleukin-2\ \ for 14 days, anti-CD3 and anti-CD28 coated beads for 14 days, 1 \u03BCg/mL Interleukin-4\ \ antibody for 36 hours, 30 ng/mL Interleukin-12 subunit alpha for 36 hours"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (35 years) treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 30 ng/mL Interleukin-12 subunit beta for 36 hours, 10 ng/mL Interleukin-2 for 14 days, anti-CD3 and anti-CD28 coated beads for 14 days, 1 μg/mL Interleukin-4 antibody for 36 hours, 30 ng/mL Interleukin-12 subunit alpha for 36 hours output_type: peaks 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 {ENCFF528SLH|/files/ENCFF528SLH/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR636DIR | float |
DNase-seq_ENCSR636DIR |
DNase-seq ENCSR636DIR [biosample_summary="Homo sapiens activated T-helper 1 cell\ \ male adult (35 years) treated with anti-CD3 and anti-CD28 coated beads for 24\ \ hours, 30 ng/mL Interleukin-12 subunit beta for 36 hours, 10 ng/mL Interleukin-2\ \ for 14 days, anti-CD3 and anti-CD28 coated beads for 14 days, 1 \u03BCg/mL Interleukin-4\ \ antibody for 36 hours, 30 ng/mL Interleukin-12 subunit alpha for 36 hours"]
|
 |
[0.116, 30] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10850862 | 0.34% | 53045 |
| chr1 | 1113245 | 0.45% | 5405 |
| chr2 | 749211 | 0.31% | 3651 |
| chr3 | 607813 | 0.31% | 2989 |
| chr4 | 378814 | 0.20% | 1852 |
| chr5 | 484004 | 0.27% | 2393 |
| chr6 | 645452 | 0.38% | 3129 |
| chr7 | 479193 | 0.30% | 2381 |
| chr8 | 409816 | 0.28% | 2056 |
| chr9 | 453546 | 0.33% | 2212 |
| chr10 | 497602 | 0.37% | 2438 |
| chr11 | 545380 | 0.40% | 2667 |
| chr12 | 561262 | 0.42% | 2733 |
| chr13 | 214930 | 0.19% | 1038 |
| chr14 | 375606 | 0.35% | 1807 |
| chr15 | 365426 | 0.36% | 1821 |
| chr16 | 444149 | 0.49% | 2165 |
| chr17 | 656083 | 0.79% | 3177 |
| chr18 | 170485 | 0.21% | 854 |
| chr19 | 668754 | 1.14% | 3174 |
| chr20 | 305822 | 0.47% | 1534 |
| chr21 | 123165 | 0.26% | 617 |
| chr22 | 270878 | 0.53% | 1315 |
| chrX | 316506 | 0.20% | 1575 |
| chrY | 13720 | 0.02% | 62 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 53045 | 1 | 820 | 204.56 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF253LML.bed.gz | 589.07 KB | 2a6658b68eeeefeb238b5a3664780ac3 |
| ENCFF253LML.tabix.bed.gz | 538.38 KB | 8c91d17c11e0e1a1e9d2005170dcbadd |
| ENCFF253LML.tabix.bed.gz.tbi | 250.8 KB | 9e23be26abb45e355a3536ae8b3f31ca |
| genomic_resource.yaml | 3.66 KB | fd54570dbbafcd66fb0888fd5646090a |
| statistics/ |