ExperimentSetReplicate

ExperimentSet4DNES7RDRS69
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

   May 15th, 2019 at 3:09pm
Source Publication
Cohesin Loss Eliminates All Loop Domains.
Rao SSP, Huang SC, et al., Cell 2017

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

18 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES7RDRS69
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIOCB8HS6
616.49m
46.114%
25.564%
28.322%
Experiment
4DNEXGPZMPL8
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)
4DNFIA2BCXBR
145.96m
45.005%
25.203%
29.792%
Experiment
4DNEX8X3TRLB
Bio Rep 1, Tec Rep 2
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIYWN7AFI
3.74m
45.167%
24.42%
30.413%
Experiment
4DNEXN961NDZ
Bio Rep 1, Tec Rep 3
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIBVPK7WR
143.49m
46.91%
24.353%
28.737%
Experiment
4DNEXVSKTEC2
Bio Rep 1, Tec Rep 4
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIHGXAN4P
3.29m
47.297%
23.664%
29.039%
Experiment
4DNEXC5F7PMZ
Bio Rep 1, Tec Rep 5
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFI8PST5ZC
171.45m
45.289%
27.441%
27.271%
Experiment
4DNEX75HUCBT
Bio Rep 1, Tec Rep 6
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIV3KPKWB
148.56m
47.385%
24.994%
27.621%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES7RDRS69
Multiple Experiments
File
Contact Matrix (mcool)
4DNFINKNVML6
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXGPZMPL8
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)
4DNFIVR26LFZ
226.92m
8.288%
8.989%
9.463%
8.936%
0.42%
Experiment
4DNEX8X3TRLB
Bio Rep 1, Tec Rep 2
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFI9M1Z7K6
5.29m
9.065%
14.22%
1.611%
4.447%
0.455%
Experiment
4DNEXN961NDZ
Bio Rep 1, Tec Rep 3
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFINCX8FN2
219.97m
8.53%
8.905%
8.685%
8.651%
0.408%
Experiment
4DNEXVSKTEC2
Bio Rep 1, Tec Rep 4
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIV4IPFNK
4.63m
9.104%
14.089%
1.455%
4.346%
0.437%
Experiment
4DNEXC5F7PMZ
Bio Rep 1, Tec Rep 5
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIV849UVC
272.5m
7.615%
9.79%
9.026%
10.651%
0.584%
Experiment
4DNEX75HUCBT
Bio Rep 1, Tec Rep 6
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIGJ1XIFX
232.96m
7.702%
9.326%
8.647%
10.556%
0.56%