ExperimentSetReplicate

ExperimentSet4DNESVGV5YDR
released
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Capture Hi-C on HAP-1 cells with deletion of region 2 E-forward and reverse CTCF sites (Crispr Clone-014, biotin-CTP tag)

   April 10th, 2017 at 1:11am
Source Publication
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.
Sanborn AL, Rao SS, et al., Proceedings of the National Academy of Sciences of the United States of America 2015

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
HAP-1
Experiment Type(s) 
Capture Hi-C
Modification Type 
Crispr
Treatment Type 
None
Assay Details 
Target: GRCh38:1:179830865-181830865 region, GRCh38:5:30999893-32999894 region, GRCh38:8:131987753-133987757 region

7 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESVGV5YDR
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI4VWKT5E
1.21m
55.435%
22.028%
22.536%
Experiment
4DNEXAKJPY9Y
Bio Rep 1, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIJVTLLVW
839.16k
55.376%
21.59%
23.035%
Experiment
4DNEXF6CEY13
Bio Rep 1, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFINYPH4LW
367.61k
55.572%
23.03%
21.398%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESVGV5YDR
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIP9J376Z
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXAKJPY9Y
Bio Rep 1, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIPW7LRYE
1.27m
6.005%
18.874%
5.303%
3.487%
1.12%
Experiment
4DNEXF6CEY13
Bio Rep 1, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFITL616WD
571.61k
5.536%
20.238%
6.71%
3.205%
2.04%