ExperimentSetReplicate

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ExperimentSet4DNESZ2PVZWR
released
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in situ Hi-C on gm12878 with MboI and bio-dATP (Tethered HiC)

   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

8 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESZ2PVZWR
Multiple Experiments
File
4DNFIXQ3BN2R
contact list-combined (pairs)
33.71 MB
-
File
4DNFI64CJUZ5
contact matrix (hic)
240.04 MB
-
File
4DNFI8FTIGIQ
contact matrix (mcool)
82.24 MB
File
4DNFINFWPY5F
compartments (bw)
207.19 kB
-
Experiment
4DNEXMDNZ7T7
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
4DNFIZMMAR5L
alignments (bam)
410.11 MB
-
File
4DNFIGJB7GV3
contact list-replicate (pairs)
19.4 MB
-
Experiment
4DNEX8J4TXKA
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
4DNFI8LBCZX3
alignments (bam)
333.4 MB
-
File
4DNFI9TJ5R3C
contact list-replicate (pairs)
15.63 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESZ2PVZWR
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIXQ3BN2R
2.41m
61.984%
18.297%
19.719%
Experiment
4DNEXMDNZ7T7
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIGJB7GV3
1.34m
61.769%
18.688%
19.543%
Experiment
4DNEX8J4TXKA
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFI9TJ5R3C
1.08m
62.251%
17.812%
19.937%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESZ2PVZWR
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI8FTIGIQ
1000; 2000; 5000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXMDNZ7T7
Bio Rep 1, Tec Rep 1
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIZMMAR5L
1.67m
5.479%
8.948%
0.462%
5.335%
0.228%
Experiment
4DNEX8J4TXKA
Bio Rep 1, Tec Rep 2
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFI8LBCZX3
1.33m
5.348%
8.894%
0.156%
4.831%
0.241%