ExperimentSetReplicate

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ExperimentSet4DNESR8I1SZG
released
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Hi-C: Hela-Kyoto cells Pro-M sync.

   February 20th, 2019 at 6:20pm
Source Publication
Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.
Wutz G, Varnai C, et al., The EMBO journal 2017

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
HeLa cell line
Experiment Type(s) 
Dilution Hi-C
Modification Type 
  1. Crispr
  2. Stable Transfection
Treatment Type 
None
Assay Details 
Enzyme: HindIII

5 Processed Files

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESR8I1SZG
Multiple Experiments
File
4DNFI5HZMQBM
contact list-combined (pairs)
4.6 GB
-
File
4DNFIF7JN3IU
contact matrix (hic)
1.49 GB
-
File
4DNFI9BA2KDU
contact matrix (mcool)
1.08 GB
Experiment
4DNEXL9BVLNW
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
4DNFIP16V8IG
alignments (bam)
44.38 GB
-
File
4DNFIQAEMB2H
contact list-replicate (pairs)
4.6 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESR8I1SZG
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI5HZMQBM
369.22m
53.92%
44.635%
1.445%
Experiment
4DNEXL9BVLNW
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
Contact List-replicate (pairs)
4DNFIQAEMB2H
369.22m
53.92%
44.635%
1.445%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESR8I1SZG
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI9BA2KDU
1000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXL9BVLNW
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
Alignments (bam)
4DNFIP16V8IG
567.51m
17.967%
13.184%
3.787%
0.001%
0.067%