ExperimentSetReplicate

ExperimentSet4DNESCOJ3ADI
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

   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
4DNESCOJ3ADI
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIIKSEZN1
627.21m
48.444%
24.357%
27.199%
Experiment
4DNEXV5DMGVC
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)
4DNFI2TI5VS5
206.21m
49.071%
23.39%
27.539%
Experiment
4DNEXSIQGF86
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)
4DNFIM5Q67AD
4.19m
49.326%
22.764%
27.909%
Experiment
4DNEXA8M4JBB
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)
4DNFINDYIYLC
122.2m
49.362%
23.238%
27.4%
Experiment
4DNEXW7984SN
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)
4DNFI961ZPPK
3.79m
49.738%
22.415%
27.847%
Experiment
4DNEX81MN4BI
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)
4DNFIN81A8QF
148.24m
47.874%
24.849%
27.277%
Experiment
4DNEXUU9N7CB
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)
4DNFI2Q3KRWE
142.57m
47.284%
26.301%
26.414%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESCOJ3ADI
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI2NUHMIM
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXV5DMGVC
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)
4DNFI4H7GGBV
312.09m
8.235%
8.709%
8.599%
8.384%
0.363%
Experiment
4DNEXSIQGF86
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)
4DNFIT18IV7X
5.88m
9.02%
13.818%
1.569%
4.262%
0.38%
Experiment
4DNEXA8M4JBB
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)
4DNFI97ESTWR
185.23m
8.283%
8.599%
8.428%
8.718%
0.333%
Experiment
4DNEXW7984SN
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)
4DNFIGA1HNI4
5.31m
8.947%
13.718%
1.561%
4.316%
0.344%
Experiment
4DNEX81MN4BI
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)
4DNFIVZZIOFY
233.63m
7.259%
9.334%
8.602%
11.356%
0.544%
Experiment
4DNEXUU9N7CB
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)
4DNFIFIZUZJR
219.85m
7.06%
9.261%
8.875%
9.955%
0.69%