ExperimentSetReplicate

ExperimentSet4DNES3JX38V5
released
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in situ Hi-C on gm12878 with MboI and bio-dATP

   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

60 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES3JX38V5
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIYECESRC
4.01 billion
53.133%
21.528%
25.339%
Experiment
4DNEX54HU8XJ
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIUOVQH68
382.06m
56.941%
23.474%
19.585%
Experiment
4DNEX5LRCIOK
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFI3O82QVV
125.26m
57.34%
20.934%
21.726%
Experiment
4DNEXNSJLJUS
Bio Rep 1, Tec Rep 3
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIIS73OJN
238.21m
57.053%
21.207%
21.741%
Experiment
4DNEXHU7XZ7R
Bio Rep 1, Tec Rep 4
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFI563E6GS
122.82m
57.841%
21.323%
20.836%
Experiment
4DNEXGT6EKP6
Bio Rep 1, Tec Rep 5
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIA38JZQ6
144.19m
54.504%
24.905%
20.591%
Experiment
4DNEXPEYBGGZ
Bio Rep 1, Tec Rep 6
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIYBWQG4A
157.34m
57.723%
18.06%
24.217%
Show 21 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES3JX38V5
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIXP4QG5B
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX54HU8XJ
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIC275NK8
486.85m
4.446%
10.597%
2.529%
3.952%
0.323%
Experiment
4DNEX5LRCIOK
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFI1LZZECL
160.65m
6.24%
10.179%
1.319%
4.295%
0.313%
Experiment
4DNEXNSJLJUS
Bio Rep 1, Tec Rep 3
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIY6GI85W
304.05m
5.832%
10.527%
1.212%
4.082%
0.313%
Experiment
4DNEXHU7XZ7R
Bio Rep 1, Tec Rep 4
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIR4LSSNY
153.77m
5.34%
10.065%
0.957%
3.765%
0.297%
Experiment
4DNEXGT6EKP6
Bio Rep 1, Tec Rep 5
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIG2Z1NYL
182.89m
5.336%
10.558%
0.962%
4.303%
0.33%
Experiment
4DNEXPEYBGGZ
Bio Rep 1, Tec Rep 6
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIPEUEWNT
212.1m
10.055%
10.277%
1.163%
4.321%
0.272%
Experiment
4DNEX456IBLL
Bio Rep 1, Tec Rep 7
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIO5EQNCG
117.63m
7.082%
10.806%
0.773%
4.098%
0.292%
Show 20 More