ExperimentSetReplicate

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ExperimentSet4DNESCIHJOXA
released
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in situ Hi-C on gm12878 with MboI and bio-dCTP (Tethered HiC)

   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) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MboI

10 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESCIHJOXA
Multiple Experiments
File
4DNFI2EK1IOQ
contact list-combined (pairs)
6.4 GB
-
File
4DNFI9YAVTI1
contact matrix (hic)
3.06 GB
-
File
4DNFITRVKRPA
contact matrix (mcool)
3.36 GB
File
4DNFIVAZEUBG
boundaries (bed)
151.46 kB
-
File
4DNFI62JTGEX
insulation score-diamond (bw)
8.14 MB
-
File
4DNFIDPK7WFE
compartments (bw)
208.31 kB
-
Experiment
4DNEX2G1IW8D
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
4DNFISDRIE2G
alignments (bam)
41.72 GB
-
File
4DNFIANAU65D
contact list-replicate (pairs)
2.61 GB
-
Experiment
4DNEXGPAWPI8
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
4DNFI76JPM3I
alignments (bam)
78.32 GB
-
File
4DNFIZTW3MEY
contact list-replicate (pairs)
4.13 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESCIHJOXA
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI2EK1IOQ
362.97m
57.021%
25.931%
17.048%
Experiment
4DNEX2G1IW8D
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIANAU65D
141.45m
58.103%
24.733%
17.165%
Experiment
4DNEXGPAWPI8
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIZTW3MEY
221.52m
56.33%
26.696%
16.974%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESCIHJOXA
Multiple Experiments
File
Contact Matrix (mcool)
4DNFITRVKRPA
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX2G1IW8D
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFISDRIE2G
202.1m
5.875%
9.927%
9.078%
5.128%
0.255%
Experiment
4DNEXGPAWPI8
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFI76JPM3I
413.23m
6.168%
9.227%
25.938%
5.061%
0.185%