ExperimentSetReplicate

ExperimentSet4DNESFNBTRO3
released
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in situ Hi-C on HCT-116 (HCT-116-RAD21-mAC), IAA treated to deplete Cohesin-Rad21 followed by 180 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
4DNESFNBTRO3
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIGEVCRU4
31.65m
55.303%
21.426%
23.271%
Experiment
4DNEXFB1XFAM
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)
4DNFIFS1538X
5.41m
58.261%
23.402%
18.338%
Experiment
4DNEXIH2VL8A
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)
4DNFIRJSLA6O
5.28m
59.205%
21.398%
19.397%
Experiment
4DNEXOTB4BES
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)
4DNFILP7UBUK
1.59m
52.536%
17.938%
29.525%
Experiment
4DNEXVJM5487
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)
4DNFILVGG7FV
1.55m
52.806%
17.734%
29.46%
Experiment
4DNEXLKPC6LE
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)
4DNFI8K4A3QC
3.36m
56.087%
19.76%
24.153%
Experiment
4DNEXPYWIJBQ
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)
4DNFIBVQ394W
3.88m
54.385%
20.341%
25.275%
Experiment
4DNEX6FH8G1J
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)
4DNFIGIP7S2K
2.41m
55.424%
22.127%
22.448%
Experiment
4DNEXLUET4T8
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)
4DNFI4SBI395
1.64m
54.645%
24.098%
21.257%
Experiment
4DNEXUEZ73BS
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)
4DNFIBR5NLC6
3.38m
50.875%
23.374%
25.751%
Experiment
4DNEXPF7FEPS
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)
4DNFINBXY1LA
3.14m
51.581%
20.748%
27.67%
Show 4 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESFNBTRO3
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIE85D1NN
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXFB1XFAM
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)
4DNFIIT4DBCX
7.47m
8.089%
13.807%
1.597%
4.08%
0.444%
Experiment
4DNEXIH2VL8A
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)
4DNFICD3VF7F
7.24m
7.901%
13.732%
1.654%
3.727%
0.403%
Experiment
4DNEXOTB4BES
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)
4DNFIQJL78CB
2.28m
7.846%
15.588%
0.774%
6.004%
0.615%
Experiment
4DNEXVJM5487
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)
4DNFI4CAB5ZR
2.2m
7.883%
15.36%
0.819%
5.553%
0.589%
Experiment
4DNEXLKPC6LE
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)
4DNFI97K8FZK
4.69m
7.507%
15.47%
1.22%
4.097%
0.474%
Experiment
4DNEXPYWIJBQ
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)
4DNFIGL8H2F5
5.48m
7.755%
15.866%
1.155%
4.392%
0.54%
Experiment
4DNEX6FH8G1J
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)
4DNFIBANKSG1
3.37m
7.94%
15.411%
0.921%
4.282%
0.545%
Experiment
4DNEXLUET4T8
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)
4DNFI1KAHJRM
2.33m
8.382%
15.627%
0.914%
4.608%
0.558%
Experiment
4DNEXUEZ73BS
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)
4DNFI3SQKYFH
4.59m
5.648%
15.211%
1.952%
3.567%
0.495%
Experiment
4DNEXPF7FEPS
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)
4DNFIXYIPI23
4.25m
5.711%
14.894%
2.006%
3.512%
0.466%