ExperimentSetReplicate

ExperimentSet4DNESEYZC9D9
released
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Capture Hi-C on wild-type HAP-1 cells

   April 10th, 2017 at 1:11am
Source Publication
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.
Sanborn AL, Rao SS, et al., Proceedings of the National Academy of Sciences of the United States of America 2015

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
HAP-1
Experiment Type(s) 
Capture Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MboI

17 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESEYZC9D9
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIG5TY53R
30.4m
59.452%
24.1%
16.449%
Experiment
4DNEXAF8PXDJ
Bio Rep 1, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIH2DFKQM
7.34m
61.356%
22.082%
16.562%
Experiment
4DNEX5H8FKJV
Bio Rep 2, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI2HTCYH7
4.21m
53.334%
29.212%
17.454%
Experiment
4DNEX9UG6UO9
Bio Rep 3, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIPMCVMBU
3.46m
54.455%
24.818%
20.727%
Experiment
4DNEXTIGW52V
Bio Rep 1, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIFH9S9J5
8.14m
60.484%
26.254%
13.262%
Experiment
4DNEX8VI8Q77
Bio Rep 4, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIEXMANLK
3.37m
63.92%
18.258%
17.822%
Experiment
4DNEX4RF5AW7
Bio Rep 4, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFISVDXLEZ
1.57m
59.581%
22.831%
17.587%
Experiment
4DNEXRIDF1WQ
Bio Rep 4, Tec Rep 3
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIJMOWTE1
2.32m
61.762%
21.926%
16.312%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESEYZC9D9
Multiple Experiments
File
Contact Matrix (mcool)
4DNFICMDXA2S
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXAF8PXDJ
Bio Rep 1, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIGFRHAY4
11.47m
6.132%
20.502%
4.429%
4.946%
1.485%
Experiment
4DNEX5H8FKJV
Bio Rep 2, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIODET89J
6.66m
6.204%
19.879%
5.995%
4.733%
1.577%
Experiment
4DNEX9UG6UO9
Bio Rep 3, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIDJBLA7Q
5.15m
5.767%
11.898%
12.856%
2.37%
0.199%
Experiment
4DNEXTIGW52V
Bio Rep 1, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIS4V7CXS
12.4m
6.993%
17.29%
5.591%
4.442%
1.042%
Experiment
4DNEX8VI8Q77
Bio Rep 4, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIYOIEGGA
4.85m
6.367%
13.925%
6.74%
3.44%
0.195%
Experiment
4DNEX4RF5AW7
Bio Rep 4, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIJZN7EDB
2.94m
5.061%
9.725%
30.032%
1.792%
0.094%
Experiment
4DNEXRIDF1WQ
Bio Rep 4, Tec Rep 3
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIA8RUFMX
3.66m
5.124%
10.331%
19.335%
1.851%
0.113%