ExperimentSetReplicate

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ExperimentSet4DNES6BKANVX
released
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Hi-C: Hela-Kyoto cells Wapl/Pds5A/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

    Explore Data

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNES6BKANVX
Multiple Experiments
File
4DNFIUQ46C65
contact list-combined (pairs)
5.16 GB
-
File
4DNFIYRROFCR
contact matrix (hic)
1.55 GB
-
File
4DNFI7VOUC33
contact matrix (mcool)
1.02 GB
File
4DNFI3QDLQNI
boundaries (bed)
188.86 kB
-
File
4DNFINE52B2M
insulation score-diamond (bw)
3.96 MB
-
File
4DNFIE2S3B4Z
compartments (bw)
206.97 kB
-
Experiment
4DNEXQFPP5S4
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
4DNFIWSP7BKF
alignments (bam)
41.92 GB
-
File
4DNFI2RIBYEW
contact list-replicate (pairs)
5.16 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNES6BKANVX
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIUQ46C65
342.75m
46.349%
48.016%
5.635%
Experiment
4DNEXQFPP5S4
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
Contact List-replicate (pairs)
4DNFI2RIBYEW
342.75m
46.349%
48.016%
5.635%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES6BKANVX
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI7VOUC33
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXQFPP5S4
Bio Rep 1, Tec Rep 1
Dilution Hi-C on HeLa cell line with HindIII
File
Alignments (bam)
4DNFIWSP7BKF
478.69m
11.452%
13.485%
3.413%
0.047%
0.078%