| Id: | DNase-seq/ENCSR044JIR |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR044JIR [biosample_summary="Homo sapiens activated naive CD8-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours"] |
| Description: |
status: released biological_replicates: Rep 1 summary: male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours output_type: peaks audit_warning: Alignment file {ENCFF187TZE|/files/ENCFF187TZE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 40054438 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 {ENCFF187TZE|/files/ENCFF187TZE/} 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_ENCSR044JIR | float |
DNase-seq_ENCSR044JIR |
DNase-seq ENCSR044JIR [biosample_summary="Homo sapiens activated naive CD8-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours"]
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[0.251, 25.2] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF459UHN.bed.gz | 340.22 KB | 0bb2777d9f45763916c5c44bbabd450e |
| ENCFF459UHN.bed.gz.dvc | 100.0 B | 80ec7444c344d7726e267eeb7142ef6d |
| ENCFF459UHN.tabix.bed.gz | 307.99 KB | 61be49f3b869506ff83e2fb844a43434 |
| ENCFF459UHN.tabix.bed.gz.dvc | 106.0 B | a96a9d0c9be6f1ae7b059895adf8f2c2 |
| ENCFF459UHN.tabix.bed.gz.tbi | 175.6 KB | 5b4ecbda56c2672a7c62868441ed7c9e |
| ENCFF459UHN.tabix.bed.gz.tbi.dvc | 110.0 B | e48808b277ee72bf24a3e314d17a8a65 |
| genomic_resource.yaml | 3.46 KB | 71a50bc51173f81266da9bbe0eb1df6d |
| genomic_resource_original.yaml | 3.24 KB | 79da962e88e73a421d0fe6713b1edd9f |
| statistics/ |