ExperimentSetReplicate

ExperimentSet4DNESK7WOJRD
released
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in situ Hi-C on HCT-116 (HCT-116-RAD21-mAC), IAA treated to deplete Cohesin-Rad21 followed by 20 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
4DNESK7WOJRD
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI6DFMB1I
29.82m
52.221%
21.103%
26.676%
Experiment
4DNEX55FMWKK
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)
4DNFI8AOQTB4
4.92m
52.605%
23.706%
23.689%
Experiment
4DNEX87PLK8L
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)
4DNFIHW4JCK1
4.2m
52.777%
24.686%
22.536%
Experiment
4DNEXZ6ES77A
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)
4DNFIZ6RAD5X
1.57m
52.492%
18.641%
28.867%
Experiment
4DNEXFFRAFEX
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)
4DNFIMEPCE8A
1.9m
51.372%
17.997%
30.63%
Experiment
4DNEX7D9CE5A
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)
4DNFIB31CP9F
2.75m
51.698%
24.883%
23.419%
Experiment
4DNEXESJX8SQ
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)
4DNFI4BXVLQS
3.7m
51.439%
25.23%
23.332%
Experiment
4DNEX2CJZ41K
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)
4DNFI7O5FGJM
2.19m
54.757%
16.996%
28.247%
Experiment
4DNEXXHRP5XX
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)
4DNFIDZ7UUMN
2.43m
51.95%
18.651%
29.399%
Experiment
4DNEXB9KSXL6
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)
4DNFIURM5R5D
2.99m
51.048%
18.463%
30.49%
Experiment
4DNEXUEE9Z3S
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)
4DNFIMK5XYXC
3.16m
52.193%
14.499%
33.308%
Show 4 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESK7WOJRD
Multiple Experiments
File
Contact Matrix (mcool)
4DNFINBNRNFT
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX55FMWKK
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)
4DNFIJH4OXPM
6.9m
8.826%
14.018%
1.65%
4.208%
0.359%
Experiment
4DNEX87PLK8L
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)
4DNFIAYSETAF
5.9m
9.001%
13.891%
1.59%
4.366%
0.36%
Experiment
4DNEXZ6ES77A
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)
4DNFIT4NUXSH
2.2m
7.72%
15.088%
0.833%
5.169%
0.549%
Experiment
4DNEXFFRAFEX
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)
4DNFIM9V2L5Y
2.7m
7.834%
15.4%
0.849%
5.49%
0.558%
Experiment
4DNEX7D9CE5A
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)
4DNFIYNOAO1N
3.87m
7.497%
15.764%
1.149%
4.418%
0.531%
Experiment
4DNEXESJX8SQ
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)
4DNFIK57BGDY
5.19m
7.724%
15.385%
1.224%
4.347%
0.558%
Experiment
4DNEX2CJZ41K
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)
4DNFIQNKUDND
3.04m
8.061%
15.078%
0.893%
3.933%
0.516%
Experiment
4DNEXXHRP5XX
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)
4DNFIWHCMLTK
3.51m
8.809%
16.01%
0.901%
4.948%
0.591%
Experiment
4DNEXB9KSXL6
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)
4DNFIHF9P4CB
4.04m
6.108%
14.258%
1.985%
3.53%
0.478%
Experiment
4DNEXUEE9Z3S
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)
4DNFI9XC9Y5F
4.22m
5.731%
13.994%
2.038%
3.269%
0.457%