ExperimentSetReplicate

ExperimentSet4DNES3QAGOZZ
released
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in situ Hi-C on HCT-116 (HCT-116-RAD21-mAC)

   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 
None
Assay Details 
Enzyme: MboI

38 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES3QAGOZZ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFITH9KJF1
2.69 billion
51.297%
19.943%
28.76%
Experiment
4DNEXPEQRJJB
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)
4DNFIDQDCBHF
417.78m
55.444%
19.676%
24.881%
Experiment
4DNEXUN3FNEX
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)
4DNFIT2UJSJE
464.86m
52.702%
22.552%
24.746%
Experiment
4DNEXRRPUVSY
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)
4DNFIE856TH8
495.93m
50.496%
22.682%
26.821%
Experiment
4DNEXJP9KPSS
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)
4DNFII4WQS3O
240.43m
50.73%
18.216%
31.054%
Experiment
4DNEXNTIZ7M9
Bio Rep 2, Tec Rep 2
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIKV1KZL9
293.9m
50.429%
18.44%
31.131%
Experiment
4DNEXCXG4HJQ
Bio Rep 2, Tec Rep 3
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFILTJ56D4
308.35m
44.188%
16.275%
39.538%
Show 10 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES3QAGOZZ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIFLDVASC
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXPEQRJJB
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)
4DNFIB28YIPF
591.78m
5.72%
8.291%
7.521%
7.871%
0.302%
Experiment
4DNEXUN3FNEX
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)
4DNFI5RZSJ3H
659.45m
5.886%
8.765%
6.992%
7.866%
0.363%
Experiment
4DNEXRRPUVSY
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)
4DNFIE8JESDT
709.54m
5.571%
8.567%
7.591%
8.376%
0.497%
Experiment
4DNEXJP9KPSS
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)
4DNFI5OQ4IME
335.56m
6.715%
8.756%
6.344%
6.535%
0.268%
Experiment
4DNEXNTIZ7M9
Bio Rep 2, Tec Rep 2
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFILHWAVN6
414.05m
6.683%
8.765%
6.913%
6.657%
0.262%
Experiment
4DNEXCXG4HJQ
Bio Rep 2, Tec Rep 3
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIP5J2V7B
432.22m
6.225%
9.023%
6.109%
7.302%
0.327%
Experiment
4DNEXPNLLZHH
Bio Rep 2, Tec Rep 4
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFI8YXC78A
333.23m
6.42%
8.79%
5.998%
6.731%
0.274%
Show 9 More