ExperimentSetReplicate

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ExperimentSet4DNESJAU6DPJ
released
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Hi-C: Hela-Kyoto cells Scc1-AID + auxin, 180 min

   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 
Chemical
Assay Details 
Enzyme: HindIII

8 Processed Files

    Explore Data

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESJAU6DPJ
Multiple Experiments
File
4DNFIBBVMCRR
contact list-combined (pairs)
1.91 GB
-
File
4DNFIZAPX6J8
contact matrix (hic)
1.15 GB
-
File
4DNFIJ28YHPI
contact matrix (mcool)
697.88 MB
File
4DNFIACSIDTD
boundaries (bed)
217.03 kB
-
File
4DNFI8ENWSXD
insulation score-diamond (bw)
3.91 MB
-
File
4DNFI3WTYTHY
compartments (bw)
205.49 kB
-
Experiment
4DNEX5O8KNYJ
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
4DNFIMGIPTOG
alignments (bam)
14.42 GB
-
File
4DNFII3DVLT4
contact list-replicate (pairs)
1.91 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESJAU6DPJ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIBBVMCRR
151.45m
36.196%
53.048%
10.756%
Experiment
4DNEX5O8KNYJ
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
Contact List-replicate (pairs)
4DNFII3DVLT4
151.45m
36.196%
53.048%
10.756%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESJAU6DPJ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIJ28YHPI
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX5O8KNYJ
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
Alignments (bam)
4DNFIMGIPTOG
202.33m
8.076%
14.684%
2.386%
0.001%
0.057%