Experiment Set

4DNESI7TK79L
released
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Capture Hi-C on HAP-1 cells with deletion of region 1 B-forward CTCF site - 2 different clones of the same modification were made to control for off-target effects.

   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 
Custom
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

10 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEXLWSXULR
Capture Hi-C on HAP-1 with MboI
File
4DNFIP7VK5O2
alignments (bam)
549.35 MB
File
4DNFIX3XYSU2
contact list-replicate (pairs)
45.17 MB
Experiment
4DNEX8SFWCYB
Capture Hi-C on HAP-1 with MboI
File
4DNFI55EJJON
alignments (bam)
680.57 MB
File
4DNFILTHMYLW
contact list-replicate (pairs)
35.67 MB
Experiment
4DNEXBAAXHZW
Capture Hi-C on HAP-1 with MboI
File
4DNFI8T3MV8Y
alignments (bam)
744.5 MB
File
4DNFI3U9YFLF
contact list-replicate (pairs)
41.52 MB
Experiment
4DNEXQ9SRQJN
Capture Hi-C on HAP-1 with MboI
File
4DNFIU9YBADW
alignments (bam)
374.01 MB
File
4DNFIU3H6H3W
contact list-replicate (pairs)
24.83 MB
Experiment
4DNEXDG1ROVP
Capture Hi-C on HAP-1 with MboI
File
4DNFIBL2R7IG
alignments (bam)
101.65 MB
File
4DNFIV4NK5UG
contact list-replicate (pairs)
8.81 MB

Quality Metrics

Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXLWSXULR
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIP7VK5O2
3.33m
6.661%
17.176%
5.739%
4.11%
2.449%
Experiment
4DNEX8SFWCYB
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI55EJJON
6.84m
6.148%
10.986%
54.212%
2.48%
0.116%
Experiment
4DNEXBAAXHZW
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI8T3MV8Y
7.08m
6.112%
10.684%
51.494%
2.47%
0.092%
Experiment
4DNEXQ9SRQJN
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIU9YBADW
2.18m
5.996%
29.306%
4.023%
7.266%
2.413%
Experiment
4DNEXDG1ROVP
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIBL2R7IG
618.41k
5.572%
17.319%
5.325%
3.382%
3.23%
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
Experiment
4DNEXLWSXULR
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIX3XYSU2
2.21m
56.826%
23.346%
19.827%
Experiment
4DNEX8SFWCYB
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFILTHMYLW
1.79m
57.932%
24.918%
17.15%
Experiment
4DNEXBAAXHZW
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI3U9YFLF
2.07m
55.517%
26.016%
18.467%
Experiment
4DNEXQ9SRQJN
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIU3H6H3W
1.17m
53.794%
13.614%
32.591%
Experiment
4DNEXDG1ROVP
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIV4NK5UG
423k
57.838%
14.293%
27.869%