ExperimentSetReplicate

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ExperimentSet4DNES51Q5X3O
released
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Hi-C: Hela-Kyoto cells Pds5SA/B RNAi

   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 
RNAi
Assay Details 
Enzyme: HindIII

8 Processed Files

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNES51Q5X3O
Multiple Experiments
File
4DNFIIDO4FAM
contact list-combined (pairs)
5.01 GB
-
File
4DNFIU95B69H
contact matrix (hic)
1.32 GB
-
File
4DNFIH7MQHOR
contact matrix (mcool)
874.92 MB
File
4DNFIE7YRIHD
boundaries (bed)
191.95 kB
-
File
4DNFI4H1MXHG
insulation score-diamond (bw)
3.97 MB
-
File
4DNFIE9K9U87
compartments (bw)
207.62 kB
-
Experiment
4DNEX9IUHCQK
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
4DNFIB1B5OJ1
alignments (bam)
37.4 GB
-
File
4DNFIHVGSUA5
contact list-replicate (pairs)
5.01 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNES51Q5X3O
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIIDO4FAM
294.56m
44.338%
50.91%
4.751%
Experiment
4DNEX9IUHCQK
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
Contact List-replicate (pairs)
4DNFIHVGSUA5
294.56m
44.338%
50.91%
4.751%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES51Q5X3O
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIH7MQHOR
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX9IUHCQK
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
Alignments (bam)
4DNFIB1B5OJ1
416.1m
10.599%
13.584%
4.93%
0.096%
0.079%