ExperimentSetReplicate

ExperimentSet4DNESUZCBCG9
released
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in situ Hi-C on HCT-116 (HCT-116-RAD21-mAC), IAA treated to deplete Cohesin-Rad21 followed by 40 min withdrawal

   November 27th, 2018 at 6:26pm
Source Publication
The Energetics and Physiological Impact of Cohesin Extrusion.
Vian L, Pekowska A, et al., Cell 2018

Assay Description  

Note on Processed Files  

Some annotated bam and pairs files generated in this Experiment Set may contain distinct reads that share the same identifier. This was caused by merging fastq files with integer identifiers (eg. @1, @2) during processing.

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
HCT116 with Crispr generated mClover and AID-tagged RAD21
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Enzyme: MboI

24 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESUZCBCG9
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIOYUB4TC
32.13m
53.936%
21.648%
24.416%
Experiment
4DNEXIMZGCE3
Bio Rep 1, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFI45WMT4C
5.92m
54.81%
24.335%
20.854%
Experiment
4DNEXT4EKUL8
Bio Rep 2, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIJ8H4216
4.94m
55.573%
21.299%
23.128%
Experiment
4DNEXQELXX5F
Bio Rep 3, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIW4WWDDR
1.34m
54.127%
19.532%
26.341%
Experiment
4DNEXLASP92J
Bio Rep 4, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIZGSUZGO
1.39m
53.329%
20.733%
25.938%
Experiment
4DNEXUS88PRH
Bio Rep 5, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFITTLYB47
3.22m
54.435%
23.3%
22.265%
Experiment
4DNEXT8435BB
Bio Rep 6, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFI8933ZN5
3.63m
53.072%
25.383%
21.545%
Experiment
4DNEX2LJ7O4H
Bio Rep 7, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIKSQ84DE
2.58m
53.093%
18.742%
28.166%
Experiment
4DNEXOX7HGSF
Bio Rep 8, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIMME86DK
2.25m
55.565%
20.084%
24.351%
Experiment
4DNEXY9AL6NK
Bio Rep 9, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFI54AL3YT
3.09m
51.999%
20.563%
27.438%
Experiment
4DNEXISZ4GBS
Bio Rep 10, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFI4HSIZ3Y
3.77m
52.176%
17.791%
30.033%
Show 4 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESUZCBCG9
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIX86CKPR
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXIMZGCE3
Bio Rep 1, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIJHGAWXC
8.21m
8.44%
13.798%
1.568%
4.134%
0.368%
Experiment
4DNEXT4EKUL8
Bio Rep 2, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIWHX7S3B
6.8m
8.714%
13.495%
1.64%
3.536%
0.315%
Experiment
4DNEXQELXX5F
Bio Rep 3, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIY8WQIOS
1.84m
7.291%
14.371%
0.859%
4.769%
0.593%
Experiment
4DNEXLASP92J
Bio Rep 4, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIMVTCQBQ
1.93m
7.134%
14.825%
0.869%
5.122%
0.597%
Experiment
4DNEXUS88PRH
Bio Rep 5, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFI7L1EPNT
4.42m
7.132%
15.181%
1.202%
3.61%
0.465%
Experiment
4DNEXT8435BB
Bio Rep 6, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIMQYT3VC
5m
7.231%
15.097%
1.238%
3.858%
0.604%
Experiment
4DNEX2LJ7O4H
Bio Rep 7, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIB8KXWDG
3.66m
8.561%
15.678%
0.908%
4.328%
0.669%
Experiment
4DNEXOX7HGSF
Bio Rep 8, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIRHLXCUV
3.16m
8.443%
15.301%
0.87%
4.223%
0.341%
Experiment
4DNEXY9AL6NK
Bio Rep 9, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIU34T9QB
4.2m
6.083%
14.577%
1.967%
3.674%
0.463%
Experiment
4DNEXISZ4GBS
Bio Rep 10, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFI16OPLL2
5.12m
6.274%
14.448%
2.008%
3.529%
0.49%