ExperimentSetReplicate

ExperimentSet4DNESOGIV7NG
released
View JSON

in situ Hi-C on HCT-116 (HCT-116-RAD21-mAC), IAA treated to deplete Cohesin-Rad21 followed by 180 min withdrawal

   May 15th, 2019 at 3:08pm
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
4DNESOGIV7NG
Multiple Experiments
File
Contact List-combined (pairs)
4DNFINNHZYZR
645.47m
51.227%
27.467%
21.306%
Experiment
4DNEXOASU8YU
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)
4DNFIC9A9AV4
139.83m
49.596%
25.508%
24.896%
Experiment
4DNEXQ9AVCA2
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)
4DNFIHRGB8Z6
13.75m
50.363%
24.348%
25.289%
Experiment
4DNEXS8HX3KW
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)
4DNFIBPO1OXW
154.32m
53.41%
22.367%
24.223%
Experiment
4DNEX5B1Y92B
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)
4DNFIQRS49EQ
14.84m
53.955%
21.45%
24.595%
Experiment
4DNEX7JVB78L
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)
4DNFIFT1KC5R
161.12m
50.101%
31.836%
18.063%
Experiment
4DNEXH8H979P
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)
4DNFICQNBCTW
161.62m
51.498%
30.494%
18.008%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESOGIV7NG
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIBSLD9S9
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXOASU8YU
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)
4DNFI4ZVUEN6
214.09m
8.362%
8.684%
9.028%
8.61%
0.385%
Experiment
4DNEXQ9AVCA2
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)
4DNFIWPZ5NL9
19.34m
8.941%
13.941%
1.783%
4.257%
0.4%
Experiment
4DNEXS8HX3KW
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)
4DNFIMA3K137
232.1m
7.517%
8.326%
9.169%
8.498%
0.405%
Experiment
4DNEX5B1Y92B
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)
4DNFICRZGKJ3
20.33m
7.889%
13.446%
1.78%
3.897%
0.419%
Experiment
4DNEX7JVB78L
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)
4DNFIBPSNKQI
242.98m
5.765%
8.977%
9.03%
9.92%
0.371%
Experiment
4DNEXH8H979P
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)
4DNFILVEMJDS
244.86m
6.047%
8.949%
8.764%
10.238%
0.36%