Experiment Set

4DNESVLZZMJ9
released
View JSON

Custom Set: GM12878 dilution 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) 
Dilution Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
  1. Enzyme: HindIII
  2. Enzyme: NcoI

8 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEXJ78M1F7
Dilution Hi-C on GM12878 with HindIII
File
4DNFIYRKYFUW
alignments (bam)
244.21 GB
File
4DNFII4JC7KV
contact list-replicate (pairs)
12.71 GB
Experiment
4DNEX17F64JD
Dilution Hi-C on GM12878 with HindIII
File
4DNFI79YNG4I
alignments (bam)
407.77 GB
File
4DNFIB13H9QZ
contact list-replicate (pairs)
25.25 GB
Experiment
4DNEX4F3JMWD
Dilution Hi-C on GM12878 with NcoI
File
4DNFI4PXFUF8
alignments (bam)
152.71 GB
File
4DNFIACGE2DJ
contact list-replicate (pairs)
9.3 GB
Experiment
4DNEXVHF97YT
Dilution Hi-C on GM12878 with HindIII
File
4DNFIBTTCCA7
alignments (bam)
590.87 GB
File
4DNFISGO7OS7
contact list-replicate (pairs)
24.9 GB

Quality Metrics

Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXJ78M1F7
Dilution Hi-C on GM12878 with HindIII
File
Alignments (bam)
4DNFIYRKYFUW
1.2 billion
5.448%
8.563%
23.238%
2.003%
0.313%
Experiment
4DNEX17F64JD
Dilution Hi-C on GM12878 with HindIII
File
Alignments (bam)
4DNFI79YNG4I
2.18 billion
8.517%
11.188%
14.551%
2.589%
0.317%
Experiment
4DNEX4F3JMWD
Dilution Hi-C on GM12878 with NcoI
File
Alignments (bam)
4DNFI4PXFUF8
670.86m
5.052%
9.525%
4.62%
2.705%
0.429%
Experiment
4DNEXVHF97YT
Dilution Hi-C on GM12878 with HindIII
File
Alignments (bam)
4DNFIBTTCCA7
2.97 billion
8.759%
8.624%
35.454%
2.997%
0.37%
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
Experiment
4DNEXJ78M1F7
Dilution Hi-C on GM12878 with HindIII
File
Contact List-replicate (pairs)
4DNFII4JC7KV
726.5m
17.494%
49.822%
32.683%
Experiment
4DNEX17F64JD
Dilution Hi-C on GM12878 with HindIII
File
Contact List-replicate (pairs)
4DNFIB13H9QZ
1.38 billion
25.265%
36.158%
38.577%
Experiment
4DNEX4F3JMWD
Dilution Hi-C on GM12878 with NcoI
File
Contact List-replicate (pairs)
4DNFIACGE2DJ
523.93m
47.197%
28.506%
24.297%
Experiment
4DNEXVHF97YT
Dilution Hi-C on GM12878 with HindIII
File
Contact List-replicate (pairs)
4DNFISGO7OS7
1.31 billion
33.07%
16.473%
50.457%