ExperimentSetReplicate

ExperimentSet4DNES4KDIQNN
released
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in situ Hi-C on HCT-116 (HCT-116-RAD21-mAC), IAA treated to deplete Cohesin-Rad21 followed by 60 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
4DNES4KDIQNN
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIDJU4NXF
573.28m
45.247%
27.057%
27.695%
Experiment
4DNEXXZC24RT
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)
4DNFIBRNLLGD
140.99m
47.931%
24.591%
27.478%
Experiment
4DNEXSCZD594
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)
4DNFIA8TNH4Y
2.55m
48.175%
24.059%
27.766%
Experiment
4DNEXC1BN6H2
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)
4DNFI2VTMPT4
145.49m
46.817%
26.317%
26.866%
Experiment
4DNEXBNYCG3A
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)
4DNFI1QRLZQB
2.8m
47.224%
25.627%
27.149%
Experiment
4DNEXL4PN2DL
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)
4DNFIBRKYI3Z
152.61m
42.378%
29.691%
27.931%
Experiment
4DNEXLGCHJ18
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)
4DNFI79GQR4R
128.84m
43.836%
27.563%
28.601%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES4KDIQNN
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIACWCWO1
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXXZC24RT
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)
4DNFIZVWSE5F
214.66m
8.657%
8.949%
9.244%
7.47%
0.385%
Experiment
4DNEXSCZD594
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)
4DNFIAERDA95
3.59m
9.254%
14.096%
1.496%
4.048%
0.404%
Experiment
4DNEXC1BN6H2
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)
4DNFIM7CNPLP
222.69m
8.835%
8.85%
9.198%
7.783%
0.35%
Experiment
4DNEXBNYCG3A
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)
4DNFIJYXRFU5
3.96m
9.542%
14.003%
1.529%
4.215%
0.368%
Experiment
4DNEXL4PN2DL
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)
4DNFIIWSCHNR
256.65m
7.934%
10.282%
9.0%
13.324%
0.365%
Experiment
4DNEXLGCHJ18
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)
4DNFICFPRMJD
214.65m
8.137%
10.096%
8.408%
13.334%
0.329%