| Id: | DNase-seq/ENCSR139PLJ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR139PLJ [biosample_summary="Homo sapiens activated CD4-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 50 U/mL Interleukin-2 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, 50 U/mL Interleukin-2 for 1 hour output_type: peaks audit_warning: Alignment file {ENCFF783MHU|/files/ENCFF783MHU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 48313964 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 {ENCFF783MHU|/files/ENCFF783MHU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR139PLJ | float |
DNase-seq_ENCSR139PLJ |
DNase-seq ENCSR139PLJ [biosample_summary="Homo sapiens activated CD4-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 50 U/mL Interleukin-2 for 1 hour"]
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[0.27, 29] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF341QVB.bed.gz | 278.21 KB | d357aaa0d9493356b7ed0d71d2390d4e |
| ENCFF341QVB.bed.gz.dvc | 100.0 B | 6f539dae650c243d927a847a7689cb19 |
| ENCFF341QVB.tabix.bed.gz | 252.87 KB | 8204173023aec60f51d55568628325b6 |
| ENCFF341QVB.tabix.bed.gz.dvc | 106.0 B | 9bf2f4787748d983cb413e9277c2c4c4 |
| ENCFF341QVB.tabix.bed.gz.tbi | 148.65 KB | a03630bff59778e05212559beb0324e9 |
| ENCFF341QVB.tabix.bed.gz.tbi.dvc | 110.0 B | 990d82dc6993660a64d1bc9ab5f95ec4 |
| genomic_resource.yaml | 3.2 KB | 003e8720226b58b5530e58e7b993e0a5 |
| genomic_resource_original.yaml | 2.99 KB | b996eb48ef7dbe0b11ba6e1a438fafb1 |
| statistics/ |