| 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: |
|
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| 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"]
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[0.443, 21.4] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF817BLK.bed.gz | 304.02 KB | e5421e57bfbd6bb7f9b4b2542591eedb |
| ENCFF817BLK.bed.gz.dvc | 100.0 B | 547539aa9acca418fbad800cf448c647 |
| ENCFF817BLK.tabix.bed.gz | 273.62 KB | 0b667873faad9698835c441d5af5f952 |
| ENCFF817BLK.tabix.bed.gz.dvc | 106.0 B | 922516beac5676d516054dc9e9cca6b4 |
| ENCFF817BLK.tabix.bed.gz.tbi | 168.29 KB | 230fbf1452c913e7856e0d780d43b82f |
| ENCFF817BLK.tabix.bed.gz.tbi.dvc | 110.0 B | 5ef2a196a84e11b032e95a6b9f4e14f5 |
| genomic_resource.yaml | 3.47 KB | 5277e15da6e76c8426c3c6fde5901f83 |
| genomic_resource_original.yaml | 3.21 KB | 23d9bf31805c828a9ba53b5bc5f34ac0 |
| statistics/ |