| Id: | DNase-seq/ENCSR133OSO |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR133OSO [biosample_summary="Homo sapiens activated CD4-positive, CD25-positive, alpha-beta regulatory T cell male adult (38 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 (38 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 {ENCFF139SFY|/files/ENCFF139SFY/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 42507818 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 {ENCFF139SFY|/files/ENCFF139SFY/} 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_ENCSR133OSO | float |
DNase-seq_ENCSR133OSO |
DNase-seq ENCSR133OSO [biosample_summary="Homo sapiens activated CD4-positive, CD25-positive, alpha-beta regulatory T cell male adult (38 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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[0.331, 34.7] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF875KTF.bed.gz | 362.91 KB | 58832492901218741a75d09891d2cffb |
| ENCFF875KTF.bed.gz.dvc | 100.0 B | f042059222a726267ed03cbdc5718680 |
| ENCFF875KTF.tabix.bed.gz | 328.57 KB | bdbd203a41c4eaaf3652ef3de8f2d9c7 |
| ENCFF875KTF.tabix.bed.gz.dvc | 106.0 B | 887d46c95e6d1db2b74b577fe703e407 |
| ENCFF875KTF.tabix.bed.gz.tbi | 182.83 KB | 3a565662abfdf56c117a51bf71a1105c |
| ENCFF875KTF.tabix.bed.gz.tbi.dvc | 110.0 B | e9c0be700ea8a70eb26cb197bab3feef |
| genomic_resource.yaml | 3.47 KB | b8b07d8b92521be89e5f1ec59fa3dc8d |
| genomic_resource_original.yaml | 3.23 KB | 3e8311d1a5d874a02fb0dea9dcc21ce1 |
| statistics/ |