ExperimentSetReplicate

ExperimentSet4DNES3CUDIXW
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Capture Hi-C on HAP-1 cells with deletion of region 1 B-reverse 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
4DNES3CUDIXW
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIQIXK1HJ
3.85m
54.799%
16.551%
28.649%
Experiment
4DNEXU67SGF3
Bio Rep 1, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI3TCHWVK
702.76k
54.61%
15.804%
29.587%
Experiment
4DNEXPUK1J27
Bio Rep 1, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI2H4JHCG
1.26m
53.154%
17.298%
29.548%
Experiment
4DNEX5PPVGJN
Bio Rep 1, Tec Rep 3
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIH8C9SZD
1.19m
56.7%
14.563%
28.737%
Experiment
4DNEX1BOSCUW
Bio Rep 1, Tec Rep 4
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIE95P87I
703.62k
54.735%
19.31%
25.955%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES3CUDIXW
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI6NCUHDC
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
4DNEXU67SGF3
Bio Rep 1, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIGJ86G9D
1.17m
6.498%
22.862%
4.293%
6.046%
1.988%
Experiment
4DNEXPUK1J27
Bio Rep 1, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI6U3ZRJO
2.13m
6.858%
23.815%
3.809%
6.346%
2.291%
Experiment
4DNEX5PPVGJN
Bio Rep 1, Tec Rep 3
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI31NSVKK
1.96m
6.864%
22.241%
3.876%
6.414%
1.623%
Experiment
4DNEX1BOSCUW
Bio Rep 1, Tec Rep 4
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIUGG5Z9S
1.32m
7.141%
27.683%
3.796%
8.051%
2.491%