Experiment Set

4DNES53X6NA3
released
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GM12878 crosslinking titration in situ Hi-C - a set of experiments representing all combinations of two different crosslinking temperatures (22 or 37 degrees centrigrade) and 3 different crosslinking times (1, 5 or 10 minutes).

   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 
Custom
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
GM12878
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MboI

12 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEXGZYWONK
in situ Hi-C on GM12878 with MboI
File
4DNFIQIWXMC9
alignments (bam)
262.74 MB
File
4DNFIA8OXKNB
contact list-replicate (pairs)
11.19 MB
Experiment
4DNEXG5TFT1O
in situ Hi-C on GM12878 with MboI
File
4DNFIQVF4H3Z
alignments (bam)
296.41 MB
File
4DNFIGKYRZBT
contact list-replicate (pairs)
10.91 MB
Experiment
4DNEXU8OXQ34
in situ Hi-C on GM12878 with MboI
File
4DNFI157JQYK
alignments (bam)
403.04 MB
File
4DNFIUAUS2H6
contact list-replicate (pairs)
14.77 MB
Experiment
4DNEX7TEPATH
in situ Hi-C on GM12878 with MboI
File
4DNFIMVZW6OV
alignments (bam)
333.76 MB
File
4DNFILXNOYC7
contact list-replicate (pairs)
15.95 MB
Experiment
4DNEXPTUMT22
in situ Hi-C on GM12878 with MboI
File
4DNFIZXSH72P
alignments (bam)
355.37 MB
File
4DNFIWO1FTN5
contact list-replicate (pairs)
16.77 MB
Experiment
4DNEXU1M7F62
in situ Hi-C on GM12878 with MboI
File
4DNFI51DAAIH
alignments (bam)
384.47 MB
File
4DNFIS8JO2QX
contact list-replicate (pairs)
16.22 MB

Quality Metrics

Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXGZYWONK
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIQIWXMC9
1.22m
22.286%
10.327%
0.045%
4.635%
0.293%
Experiment
4DNEXG5TFT1O
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIQVF4H3Z
1.41m
32.748%
8.561%
0.036%
5.188%
0.255%
Experiment
4DNEXU8OXQ34
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFI157JQYK
1.9m
32.645%
9.28%
0.04%
5.996%
0.242%
Experiment
4DNEX7TEPATH
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIMVZW6OV
1.55m
14.398%
10.292%
0.075%
3.818%
0.302%
Experiment
4DNEXPTUMT22
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIZXSH72P
1.63m
14.226%
11.008%
0.068%
4.452%
0.362%
Experiment
4DNEXU1M7F62
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFI51DAAIH
1.78m
22.853%
10.225%
0.049%
5.048%
0.287%
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
Experiment
4DNEXGZYWONK
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIA8OXKNB
763.8k
44.751%
32.112%
23.137%
Experiment
4DNEXG5TFT1O
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIGKYRZBT
752.86k
43.768%
41.28%
14.952%
Experiment
4DNEXU8OXQ34
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIUAUS2H6
987.78k
45.739%
27.103%
27.157%
Experiment
4DNEX7TEPATH
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFILXNOYC7
1.11m
47.033%
35.094%
17.873%
Experiment
4DNEXPTUMT22
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIWO1FTN5
1.15m
49.578%
27.464%
22.958%
Experiment
4DNEXU1M7F62
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIS8JO2QX
1.1m
50.635%
26.037%
23.328%