ExperimentSetReplicate

ExperimentSet4DNESJV9TH8Q
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in situ Hi-C on HCT-116 (HCT-116-RAD21-mAC), IAA treated for 360 min to deplete Cohesin-Rad21

   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

36 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESJV9TH8Q
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI2X45Z5L
2.55 billion
48.794%
17.198%
34.007%
Experiment
4DNEXV5XW8B8
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)
4DNFIR7Q949M
287.75m
57.801%
14.865%
27.334%
Experiment
4DNEXRQCSCJW
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)
4DNFIQA9LNI9
322m
56.87%
16.497%
26.633%
Experiment
4DNEXMSLJGGQ
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)
4DNFI7NWWWNA
460.54m
46.194%
15.965%
37.841%
Experiment
4DNEX7I6TGN1
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)
4DNFI5HOVNFS
323.88m
44.027%
17.087%
38.885%
Experiment
4DNEX2SQOA65
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)
4DNFICOPDAE8
262.85m
41.693%
17.156%
41.151%
Experiment
4DNEXZCZIQ2A
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)
4DNFIIMOHDU7
305.64m
47.485%
18.839%
33.676%
Show 9 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESJV9TH8Q
Multiple Experiments
File
Contact Matrix (mcool)
4DNFILP99QJS
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXV5XW8B8
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)
4DNFI9EHYW7A
402.25m
5.559%
8.239%
7.076%
7.593%
0.359%
Experiment
4DNEXRQCSCJW
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)
4DNFISTMAAG8
453.6m
5.743%
8.441%
6.991%
7.838%
0.347%
Experiment
4DNEXMSLJGGQ
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)
4DNFIMO766R4
664.78m
6.149%
9.177%
7.135%
8.261%
0.597%
Experiment
4DNEX7I6TGN1
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)
4DNFI4HE83XW
467.41m
7.375%
9.062%
7.339%
6.931%
0.3%
Experiment
4DNEX2SQOA65
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)
4DNFIQPZASBK
377.99m
7.448%
9.289%
6.693%
7.03%
0.32%
Experiment
4DNEXZCZIQ2A
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)
4DNFIYK5EPVW
436.94m
7.41%
8.987%
6.719%
6.934%
0.283%
Experiment
4DNEXSR3I82C
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)
4DNFIWNFXNDA
562.19m
7.019%
8.91%
7.421%
7.013%
0.283%
Show 8 More