ExperimentSetReplicate

ExperimentSet4DNESBJ1KYYH
released
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in situ Hi-C on gm12878 with NcoI and bio-dCTP

   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

12 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESBJ1KYYH
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIE7D8Z3N
23.22m
56.305%
26.304%
17.391%
Experiment
4DNEX681LMAK
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with NcoI
File
Contact List-replicate (pairs)
4DNFI3LLFMRY
2.68m
60.278%
20.228%
19.493%
Experiment
4DNEXY1C3Y6L
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with NcoI
File
Contact List-replicate (pairs)
4DNFILQHCGXX
10.92m
55.19%
27.094%
17.717%
Experiment
4DNEX1OOVTSS
Bio Rep 1, Tec Rep 3
in situ Hi-C on GM12878 with NcoI
File
Contact List-replicate (pairs)
4DNFIRLQPS87
4.67m
55.382%
27.985%
16.633%
Experiment
4DNEXV32FZGK
Bio Rep 1, Tec Rep 4
in situ Hi-C on GM12878 with NcoI
File
Contact List-replicate (pairs)
4DNFIMGZ4MRQ
4.96m
57.482%
26.266%
16.252%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESBJ1KYYH
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIBKJ25D4
5000; 10000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX681LMAK
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with NcoI
File
Alignments (bam)
4DNFISDS17NX
3.29m
6.388%
8.317%
0.16%
3.581%
0.479%
Experiment
4DNEXY1C3Y6L
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with NcoI
File
Alignments (bam)
4DNFI7G9WV5L
18.2m
7.272%
4.442%
0.683%
27.631%
0.735%
Experiment
4DNEX1OOVTSS
Bio Rep 1, Tec Rep 3
in situ Hi-C on GM12878 with NcoI
File
Alignments (bam)
4DNFICKUDD5K
5.91m
6.268%
10.413%
0.311%
3.986%
0.452%
Experiment
4DNEXV32FZGK
Bio Rep 1, Tec Rep 4
in situ Hi-C on GM12878 with NcoI
File
Alignments (bam)
4DNFIL5XAZ5O
6.07m
5.558%
9.229%
0.12%
3.351%
0.381%