| 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: |
|
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| 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"]
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[0.496, 23.7] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF083CXT.bed.gz | 279.45 KB | 117d2c89d2773f7598dba94ad25e3b40 |
| ENCFF083CXT.bed.gz.dvc | 100.0 B | 641de5539a66181a423761026c5aa05e |
| ENCFF083CXT.tabix.bed.gz | 252.82 KB | a90b32c7499eb63ac318ed0b7989cb64 |
| ENCFF083CXT.tabix.bed.gz.dvc | 106.0 B | 4a7b03cb7fa115dd61067a32d25f3776 |
| ENCFF083CXT.tabix.bed.gz.tbi | 151.96 KB | 240a455db8f381033bb9c7e0f35aab3a |
| ENCFF083CXT.tabix.bed.gz.tbi.dvc | 110.0 B | ca1d86fc2b5288d9700c52311a9f5c50 |
| genomic_resource.yaml | 3.27 KB | 32c1efce25122edb32030ec42f25e28e |
| genomic_resource_original.yaml | 3.04 KB | e8c2073039c0b9c69c8ccc6bae34f7b2 |
| statistics/ |