ExperimentSetReplicate

ExperimentSet4DNESUTEOMGQ
released
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in situ Hi-C on HAP-1 cells used to generate-wide wild-type Hi-C map

   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

Assay Description  

Experiment Set Properties  

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

16 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESUTEOMGQ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIWGGYEW2
752.29m
54.306%
29.048%
16.646%
Experiment
4DNEXHSQ1DTV
Bio Rep 1, Tec Rep 1
in situ Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI4Y4Z7AF
193.74m
51.097%
31.157%
17.747%
Experiment
4DNEXLZJN8LZ
Bio Rep 1, Tec Rep 2
in situ Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI2HTENAI
147.57m
51.856%
30.956%
17.188%
Experiment
4DNEX5NCT8WI
Bio Rep 1, Tec Rep 3
in situ Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIWO14LYW
143.94m
50.786%
31.578%
17.636%
Experiment
4DNEXASVIO87
Bio Rep 2, Tec Rep 1
in situ Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFISQCBGL1
132.13m
58.775%
26.644%
14.581%
Experiment
4DNEXN16TEZZ
Bio Rep 3, Tec Rep 1
in situ Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIMYACUIM
134.91m
60.974%
23.586%
15.439%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESUTEOMGQ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFINSKEZND
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXHSQ1DTV
Bio Rep 1, Tec Rep 1
in situ Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFICQ95BOP
270.22m
6.829%
12.202%
1.425%
7.847%
0.531%
Experiment
4DNEXLZJN8LZ
Bio Rep 1, Tec Rep 2
in situ Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIKWPZ4U5
240.46m
18.632%
11.136%
0.843%
8.02%
0.474%
Experiment
4DNEX5NCT8WI
Bio Rep 1, Tec Rep 3
in situ Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIHBBU3RC
224.54m
16.179%
11.235%
0.772%
7.71%
0.449%
Experiment
4DNEXASVIO87
Bio Rep 2, Tec Rep 1
in situ Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI5MQUCRI
179.26m
6.315%
8.765%
3.072%
8.141%
0.35%
Experiment
4DNEXN16TEZZ
Bio Rep 3, Tec Rep 1
in situ Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI97YJKKH
181.31m
6.293%
8.481%
2.999%
7.818%
0.267%