Experiment Set

4DNESIG3U3KX
released
View JSON

Custom Set: GM12878 pellet/supernatant Hi-C

   April 9th, 2017 at 5:34pm
Source Publication
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Rao SS, Huntley MH, et al., Cell 2014

Assay Description  

Experiment Set Properties  

Set Type 
Custom
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
GM12878
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MboI

4 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEXRNJMGNI
in situ Hi-C on GM12878 with MboI
File
4DNFIOJB13JQ
alignments (bam)
12.89 GB
File
4DNFIXUCQWSJ
contact list-replicate (pairs)
642.99 MB
Experiment
4DNEXMHA9FL9
in situ Hi-C on GM12878 with MboI
File
4DNFIC5J93VV
alignments (bam)
20.31 GB
File
4DNFIUVGBN25
contact list-replicate (pairs)
1.14 GB

Quality Metrics

Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXRNJMGNI
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIOJB13JQ
75.26m
11.015%
12.491%
23.492%
9.568%
2.626%
Experiment
4DNEXMHA9FL9
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIC5J93VV
99.39m
14.496%
10.031%
0.48%
14.267%
0.187%
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
Experiment
4DNEXRNJMGNI
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIXUCQWSJ
32.69m
8.694%
31.053%
60.253%
Experiment
4DNEXMHA9FL9
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIUVGBN25
60.35m
49.031%
29.173%
21.796%