ExperimentSetReplicate

ExperimentSet4DNES4269GKX
released
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in situ Hi-C on gm12878 with MboI and bio-dATP (in agar plugs, w/out crosslinking)

   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

14 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES4269GKX
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIWE8W2WS
144.39m
15.758%
44.401%
39.841%
Experiment
4DNEXX2K39AC
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFI7E69FHJ
42.18m
18.54%
43.543%
37.917%
Experiment
4DNEX4EWVTPF
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIQQRRQSP
21.62m
12.83%
55.368%
31.802%
Experiment
4DNEXWUUDBZN
Bio Rep 1, Tec Rep 3
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFI74S4R6N
51.91m
18.243%
36.955%
44.802%
Experiment
4DNEXKDQWHYT
Bio Rep 1, Tec Rep 4
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFI5G9HJMT
28.69m
9.377%
50.871%
39.752%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES4269GKX
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI2ZUCIHD
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXX2K39AC
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIVZDYRQL
59.37m
7.705%
12.611%
2.102%
6.544%
0.594%
Experiment
4DNEX4EWVTPF
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIDT3L96H
39.95m
23.499%
21.248%
0.871%
0.259%
0.324%
Experiment
4DNEXWUUDBZN
Bio Rep 1, Tec Rep 3
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIVPFKHDG
65.56m
4.032%
12.669%
0.543%
3.583%
0.569%
Experiment
4DNEXKDQWHYT
Bio Rep 1, Tec Rep 4
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFI2WWQUO7
49.79m
12.609%
25.139%
4.498%
0.146%
0.367%