Experiment Set

4DNESURWI8WR
released
View JSON

Custom Set: GM12878 in-situ Hi-C (no crosslinking)

   April 9th, 2017 at 5:34pm
Source Publication
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Rao SS, Huntley MH, et al., Cell 2014

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

10 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEXHGRTX1A
in situ Hi-C on GM12878 with MboI
File
4DNFI9XZ1R1R
alignments (bam)
20.62 GB
File
4DNFIO9HS2U4
contact list-replicate (pairs)
1.81 GB
Experiment
4DNEXX2K39AC
in situ Hi-C on GM12878 with MboI
File
4DNFIVZDYRQL
alignments (bam)
10.24 GB
File
4DNFI7E69FHJ
contact list-replicate (pairs)
810.93 MB
Experiment
4DNEXWUUDBZN
in situ Hi-C on GM12878 with MboI
File
4DNFIVPFKHDG
alignments (bam)
10.5 GB
File
4DNFI74S4R6N
contact list-replicate (pairs)
1009.91 MB
Experiment
4DNEX4EWVTPF
in situ Hi-C on GM12878 with MboI
File
4DNFIDT3L96H
alignments (bam)
3.98 GB
File
4DNFIQQRRQSP
contact list-replicate (pairs)
420.54 MB
Experiment
4DNEXKDQWHYT
in situ Hi-C on GM12878 with MboI
File
4DNFI2WWQUO7
alignments (bam)
4.67 GB
File
4DNFI5G9HJMT
contact list-replicate (pairs)
552.34 MB

Quality Metrics

Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXHGRTX1A
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFI9XZ1R1R
130.38m
8.182%
8.559%
3.404%
2.946%
0.311%
Experiment
4DNEXX2K39AC
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIVZDYRQL
59.37m
7.705%
12.611%
2.102%
6.544%
0.594%
Experiment
4DNEXWUUDBZN
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIVPFKHDG
65.56m
4.032%
12.669%
0.543%
3.583%
0.569%
Experiment
4DNEX4EWVTPF
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIDT3L96H
39.95m
23.499%
21.248%
0.871%
0.259%
0.324%
Experiment
4DNEXKDQWHYT
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFI2WWQUO7
49.79m
12.609%
25.139%
4.498%
0.146%
0.367%
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
Experiment
4DNEXHGRTX1A
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIO9HS2U4
100.28m
15.989%
51.881%
32.129%
Experiment
4DNEXX2K39AC
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFI7E69FHJ
42.18m
18.54%
43.543%
37.917%
Experiment
4DNEXWUUDBZN
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFI74S4R6N
51.91m
18.243%
36.955%
44.802%
Experiment
4DNEX4EWVTPF
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIQQRRQSP
21.62m
12.83%
55.368%
31.802%
Experiment
4DNEXKDQWHYT
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFI5G9HJMT
28.69m
9.377%
50.871%
39.752%