ExperimentSetReplicate

ExperimentSet4DNESSCS4D46
released
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in situ Hi-C on gm12878 with NcoI and bio-dCTP (Tethered HiC, high ligation volume)

   April 9th, 2017 at 5:35pm
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) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: NcoI

6 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESSCS4D46
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIUS2SHOT
1.32m
52.399%
26.366%
21.234%
Experiment
4DNEXECG9AQA
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with NcoI
File
Contact List-replicate (pairs)
4DNFIUYPWCPS
1.32m
52.399%
26.366%
21.234%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESSCS4D46
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIY3OLS32
1000; 2000; 5000; 10000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXECG9AQA
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with NcoI
File
Alignments (bam)
4DNFISVGXZTJ
1.59m
5.476%
8.578%
0.227%
2.949%
0.351%