ExperimentSetReplicate

ExperimentSet4DNESG4XBHWB
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Capture Hi-C on HAP-1 cells with deletion of region 1 A-forward CTCF site

   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

11 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESG4XBHWB
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIXZQSFQZ
33.02m
54.9%
24.113%
20.987%
Experiment
4DNEXV22N38P
Bio Rep 1, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI4PQ4BSE
9.09m
53.771%
24.356%
21.873%
Experiment
4DNEX23TSUEX
Bio Rep 1, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI4SLDM4I
5.88m
54.606%
23.373%
22.02%
Experiment
4DNEXFHWUX8H
Bio Rep 1, Tec Rep 3
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI2MWGKFU
9.61m
55.31%
23.975%
20.715%
Experiment
4DNEXTJBAHTN
Bio Rep 1, Tec Rep 4
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI49Q1SBS
8.45m
55.853%
24.524%
19.623%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESG4XBHWB
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIYRMF6YD
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
4DNEXV22N38P
Bio Rep 1, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFICPVHHLD
14.67m
6.555%
20.885%
4.875%
5.77%
0.311%
Experiment
4DNEX23TSUEX
Bio Rep 1, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIXHJNS72
11.85m
6.055%
19.762%
20.248%
4.343%
0.35%
Experiment
4DNEXFHWUX8H
Bio Rep 1, Tec Rep 3
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFILRJ5OEF
14.73m
5.928%
21.063%
2.629%
5.164%
0.399%
Experiment
4DNEXTJBAHTN
Bio Rep 1, Tec Rep 4
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI5VY4ONH
12.83m
6.027%
19.617%
3.512%
4.989%
0.304%