| Id: | DNase-seq/ENCSR442SDV |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR442SDV [biosample_summary="Homo sapiens activated CD8-positive, alpha-beta memory T cell female adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 48 hours"] |
| Description: |
status: released biological_replicates: Rep 1 summary: female adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 48 hours output_type: peaks audit_warning: Alignment file {ENCFF398QOP|/files/ENCFF398QOP/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 48832594 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 {ENCFF398QOP|/files/ENCFF398QOP/} 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: |
|
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR442SDV | float |
DNase-seq_ENCSR442SDV |
DNase-seq ENCSR442SDV [biosample_summary="Homo sapiens activated CD8-positive, alpha-beta memory T cell female adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 48 hours"]
|
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[0.226, 11.6] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF810ZJY.bed.gz | 326.56 KB | d0fa1cc1db1d358fa5c2f1bddbd46400 |
| ENCFF810ZJY.bed.gz.dvc | 100.0 B | 6abd7eb5461ed2befe6a27e0005335d5 |
| ENCFF810ZJY.tabix.bed.gz | 304.06 KB | 894bd8001db508ae79e9387cb2dbe474 |
| ENCFF810ZJY.tabix.bed.gz.dvc | 106.0 B | 25ef76d647c0a75c3f1c5f9f8b547951 |
| ENCFF810ZJY.tabix.bed.gz.tbi | 163.83 KB | aeeec3d1812ee5110c1b0d7e654f5e6f |
| ENCFF810ZJY.tabix.bed.gz.tbi.dvc | 110.0 B | 04b111f50af65559c6c4553b54edff21 |
| genomic_resource.yaml | 3.08 KB | 67727e382567585ee0c4deed1b8648aa |
| genomic_resource_original.yaml | 2.89 KB | 57d6b191e3e82c9d195eb1b110907256 |
| statistics/ |