ExperimentSetReplicate

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ExperimentSet4DNESLQG7ZKJ
released
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in situ Hi-C on gm12878 with MboI and bio-dATP (Tethered HiC, high ligation volume)

   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

8 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESLQG7ZKJ
Multiple Experiments
File
4DNFIUHPB9VC
contact list-combined (pairs)
4.01 GB
-
File
4DNFIOCW5AEM
contact matrix (hic)
2.42 GB
-
File
4DNFI46OLTQE
contact matrix (mcool)
2.56 GB
File
4DNFIJIQLMLZ
boundaries (bed)
157.59 kB
-
File
4DNFIKREI72V
insulation score-diamond (bw)
8.1 MB
-
File
4DNFI3VXZ48N
compartments (bw)
207.25 kB
-
Experiment
4DNEXT7WEQ49
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
4DNFIZO3GZRX
alignments (bam)
63.33 GB
-
File
4DNFI2I5JC3L
contact list-replicate (pairs)
4.01 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESLQG7ZKJ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIUHPB9VC
216.36m
59.393%
18.54%
22.068%
Experiment
4DNEXT7WEQ49
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFI2I5JC3L
216.36m
59.393%
18.54%
22.068%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESLQG7ZKJ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI46OLTQE
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXT7WEQ49
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIZO3GZRX
314.31m
4.754%
10.346%
11.764%
4.299%
0.216%