Experiment Set

4DNESJ8X1A2B
released
View JSON

Capture Hi-C on HAP-1 cells with region 3 H-forward CTCF site deletion - Both used the same clone. 2 different biotinylated bases (ATP, UTP) were used for tagging.

   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

4 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEX2VTRKTP
Capture Hi-C on HAP-1 with MboI
File
4DNFI3OHBT1D
alignments (bam)
827.31 MB
File
4DNFIQUDP8EU
contact list-replicate (pairs)
58.8 MB
Experiment
4DNEXQXUGDXG
Capture Hi-C on HAP-1 with MboI
File
4DNFIBHMK1NL
alignments (bam)
630.55 MB
File
4DNFIZPYZTBX
contact list-replicate (pairs)
48.28 MB

Quality Metrics

Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX2VTRKTP
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI3OHBT1D
5.49m
5.525%
27.546%
8.453%
6.226%
3.454%
Experiment
4DNEXQXUGDXG
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIBHMK1NL
4.32m
6.635%
18.253%
14.879%
5.236%
1.598%
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
Experiment
4DNEX2VTRKTP
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIQUDP8EU
2.87m
45.157%
28.99%
25.853%
Experiment
4DNEXQXUGDXG
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIZPYZTBX
2.37m
55.047%
20.905%
24.048%