ExperimentSetReplicate

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ExperimentSet4DNES3RHDBBR
released
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in situ Hi-C on gm12878 with MboI and bio-dATP (Tethered HiC, lower 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: MboI

12 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNES3RHDBBR
Multiple Experiments
File
4DNFIBEXHYG2
contact list-combined (pairs)
108.75 MB
-
File
4DNFIFX1XYKZ
contact matrix (hic)
351.4 MB
-
File
4DNFI9PIEPQA
contact matrix (mcool)
147.4 MB
File
4DNFI4GRUDCL
compartments (bw)
208.88 kB
-
Experiment
4DNEXNMDXSP1
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
4DNFIDSOGHLM
alignments (bam)
610.55 MB
-
File
4DNFIA32ODXZ
contact list-replicate (pairs)
30.47 MB
-
Experiment
4DNEXYNM1II5
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
4DNFI3FIHUXZ
alignments (bam)
555.73 MB
-
File
4DNFIAK2SX23
contact list-replicate (pairs)
26.41 MB
-
Experiment
4DNEXT3VJDNU
Bio Rep 1, Tec Rep 3
in situ Hi-C on GM12878 with MboI
File
4DNFI84Q8HXC
alignments (bam)
649.88 MB
-
File
4DNFIMEIXLSE
contact list-replicate (pairs)
30.38 MB
-
Experiment
4DNEXWGWFK1T
Bio Rep 1, Tec Rep 4
in situ Hi-C on GM12878 with MboI
File
4DNFIIV1353G
alignments (bam)
580.1 MB
-
File
4DNFIH6KL2OT
contact list-replicate (pairs)
27 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNES3RHDBBR
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIBEXHYG2
8.13m
37.838%
42.711%
19.45%
Experiment
4DNEXNMDXSP1
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIA32ODXZ
2.19m
32.176%
47.389%
20.434%
Experiment
4DNEXYNM1II5
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIAK2SX23
1.84m
48.351%
29.803%
21.846%
Experiment
4DNEXT3VJDNU
Bio Rep 1, Tec Rep 3
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIMEIXLSE
2.17m
36.477%
45.368%
18.155%
Experiment
4DNEXWGWFK1T
Bio Rep 1, Tec Rep 4
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIH6KL2OT
1.93m
35.776%
46.707%
17.517%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES3RHDBBR
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI9PIEPQA
1000; 2000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXNMDXSP1
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIDSOGHLM
2.63m
3.782%
9.511%
0.44%
3.233%
0.614%
Experiment
4DNEXYNM1II5
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFI3FIHUXZ
2.24m
4.773%
9.02%
0.268%
4.104%
0.357%
Experiment
4DNEXT3VJDNU
Bio Rep 1, Tec Rep 3
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFI84Q8HXC
2.66m
4.973%
9.248%
0.473%
3.588%
0.521%
Experiment
4DNEXWGWFK1T
Bio Rep 1, Tec Rep 4
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIIV1353G
2.36m
4.698%
9.103%
0.778%
3.56%
0.422%