Experiment Set

4DNES1WJGQEG
released
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Capture Hi-C on HAP-1 cells with deletion of region 2 E-forward CTCF site - 4 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
4DNEXCVXZY97
Capture Hi-C on HAP-1 with MboI
File
4DNFIOJU9X8Q
alignments (bam)
3.3 GB
File
4DNFIAMWRV1G
contact list-replicate (pairs)
288.04 MB
Experiment
4DNEXLFZA8EQ
Capture Hi-C on HAP-1 with MboI
File
4DNFI1GSY76G
alignments (bam)
6.76 GB
File
4DNFIFRBPPVE
contact list-replicate (pairs)
467.57 MB
Experiment
4DNEXHG5WSK5
Capture Hi-C on HAP-1 with MboI
File
4DNFI45NOO1E
alignments (bam)
2.1 GB
File
4DNFIBIDW6KL
contact list-replicate (pairs)
139.99 MB
Experiment
4DNEX88KQH75
Capture Hi-C on HAP-1 with MboI
File
4DNFIKVUDXAV
alignments (bam)
835.08 MB
File
4DNFIROD4C9U
contact list-replicate (pairs)
67.24 MB
Experiment
4DNEX9GCPXZN
Capture Hi-C on HAP-1 with MboI
File
4DNFISMZFKSW
alignments (bam)
602.22 MB
File
4DNFIXSRR92O
contact list-replicate (pairs)
49.62 MB

Quality Metrics

Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXCVXZY97
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIOJU9X8Q
25.95m
7.77%
17.19%
17.127%
2.17%
0.471%
Experiment
4DNEXLFZA8EQ
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI1GSY76G
58.73m
7.597%
18.162%
31.694%
2.252%
0.456%
Experiment
4DNEXHG5WSK5
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI45NOO1E
19.3m
9.078%
12.656%
40.355%
1.562%
0.102%
Experiment
4DNEX88KQH75
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIKVUDXAV
4.95m
6.885%
19.705%
2.102%
4.909%
1.026%
Experiment
4DNEX9GCPXZN
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFISMZFKSW
3.59m
6.488%
18.842%
2.389%
4.642%
1.067%
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
Experiment
4DNEXCVXZY97
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIAMWRV1G
14.46m
62.632%
22.125%
15.243%
Experiment
4DNEXLFZA8EQ
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIFRBPPVE
23.67m
63.56%
21.641%
14.799%
Experiment
4DNEXHG5WSK5
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIBIDW6KL
7.01m
64.972%
19.89%
15.139%
Experiment
4DNEX88KQH75
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIROD4C9U
3.29m
57.6%
25.998%
16.402%
Experiment
4DNEX9GCPXZN
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIXSRR92O
2.43m
59.927%
26.145%
13.928%