ExperimentSetReplicate

Browser Suggestion

Google Chrome  or Mozilla Firefox are the recommended browser(s) for using the 4DN Data Portal.

Microsoft Edge, Safari, Opera etc. should work for a majority of portal functions but are not explicitly supported and may present some glitches, e.g. during submission.

ExperimentSet4DNESNDJ9QVX
released
View JSON

dilution Hi-C on gm12878 with NcoI and bio-dCTP

   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 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
GM12878
Experiment Type(s) 
Dilution Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: NcoI

8 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESNDJ9QVX
Multiple Experiments
File
4DNFIES3S7VJ
contact list-combined (pairs)
9.3 GB
-
File
4DNFIPAI8XB5
contact matrix (hic)
4.01 GB
-
File
4DNFIZAWQ34F
contact matrix (mcool)
4.41 GB
File
4DNFINIKXWQN
boundaries (bed)
134.82 kB
-
File
4DNFIHSA1H9M
insulation score-diamond (bw)
2.42 MB
-
File
4DNFIJEZA4FV
compartments (bw)
208.92 kB
-
Experiment
4DNEX4F3JMWD
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM12878 with NcoI
File
4DNFI4PXFUF8
alignments (bam)
152.71 GB
-
File
4DNFIACGE2DJ
contact list-replicate (pairs)
9.3 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESNDJ9QVX
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIES3S7VJ
523.93m
47.197%
28.506%
24.297%
Experiment
4DNEX4F3JMWD
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM12878 with NcoI
File
Contact List-replicate (pairs)
4DNFIACGE2DJ
523.93m
47.197%
28.506%
24.297%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESNDJ9QVX
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIZAWQ34F
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX4F3JMWD
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM12878 with NcoI
File
Alignments (bam)
4DNFI4PXFUF8
670.86m
5.052%
9.525%
4.62%
2.705%
0.429%