| Id: | DNase-seq/ENCSR618HFT |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR618HFT [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 1 hour, 100 ng/mL TNF-alpha for 1 hour"] |
| Description: |
status: released biological_replicates: Rep 1 summary: male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL TNF-alpha for 1 hour output_type: peaks audit_warning: Alignment file {ENCFF159XDU|/files/ENCFF159XDU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 21661012 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 {ENCFF159XDU|/files/ENCFF159XDU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 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: |
|
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR618HFT | float |
DNase-seq_ENCSR618HFT |
DNase-seq ENCSR618HFT [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 1 hour, 100 ng/mL TNF-alpha for 1 hour"]
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[0.371, 52.1] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF992ZCX.bed.gz | 276.8 KB | 3db7e01483f447fb35b1d29d65709d99 |
| ENCFF992ZCX.bed.gz.dvc | 100.0 B | 4c0bd38e97795a5df22f93af29784872 |
| ENCFF992ZCX.tabix.bed.gz | 248.08 KB | 38b837576f5b4e5fd72406831fc015f4 |
| ENCFF992ZCX.tabix.bed.gz.dvc | 106.0 B | 79d391df588e6b8712153136b239cda8 |
| ENCFF992ZCX.tabix.bed.gz.tbi | 154.36 KB | 590aa05377976295be7e9677dde00512 |
| ENCFF992ZCX.tabix.bed.gz.tbi.dvc | 110.0 B | 13176191900b158dff704f801a901782 |
| genomic_resource.yaml | 3.22 KB | f3639b68d43f44489cf38de1c0528cfd |
| genomic_resource_original.yaml | 3.01 KB | fee32e7eeb7b81c1808196aabd347bb5 |
| statistics/ |