ExperimentSetReplicate

ExperimentSet4DNES4296C5Q
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Imr90 dilution Hi-C experiments from Jin et al (GSE43070)

   May 12th, 2017 at 4:31pm
Source Publication
A high-resolution map of the three-dimensional chromatin interactome in human cells.
Jin F, Li Y, et al., Nature 2013

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 
primary cells
Sample 
IMR-90
Experiment Type(s) 
Dilution Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: HindIII

18 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES4296C5Q
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI25TK6MT
1.07 billion
24.19%
50.352%
25.458%
Experiment
4DNEXYXFH266
Bio Rep 1, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Contact List-replicate (pairs)
4DNFIREXVV6S
176.01m
36.154%
40.651%
23.194%
Experiment
4DNEX8QF8KNE
Bio Rep 2, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Contact List-replicate (pairs)
4DNFITW2EGPF
229.45m
37.128%
21.791%
41.081%
Experiment
4DNEX9FSLNEX
Bio Rep 3, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Contact List-replicate (pairs)
4DNFISNS2EBY
242.85m
13.749%
64.032%
22.219%
Experiment
4DNEXJTZG9TO
Bio Rep 4, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Contact List-replicate (pairs)
4DNFI7KA982D
176.34m
15.312%
65.143%
19.546%
Experiment
4DNEX7BWFLX4
Bio Rep 5, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Contact List-replicate (pairs)
4DNFI1PYJDJX
137.22m
17.912%
65.186%
16.902%
Experiment
4DNEXEKL694J
Bio Rep 6, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Contact List-replicate (pairs)
4DNFIE41V9R6
105.87m
23.133%
53.134%
23.733%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES4296C5Q
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIJIP5BJF
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXYXFH266
Bio Rep 1, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Alignments (bam)
4DNFI61HD8NE
397.19m
21.098%
16.102%
18.486%
0.0%
0.085%
Experiment
4DNEX8QF8KNE
Bio Rep 2, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Alignments (bam)
4DNFISF37CTF
440.24m
18.356%
16.729%
12.796%
0.0%
0.141%
Experiment
4DNEX9FSLNEX
Bio Rep 3, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Alignments (bam)
4DNFIDVHDU1M
621.09m
10.017%
18.593%
32.289%
0.001%
0.126%
Experiment
4DNEXJTZG9TO
Bio Rep 4, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Alignments (bam)
4DNFI51PZNR9
529.16m
7.905%
16.425%
42.343%
0.002%
0.076%
Experiment
4DNEX7BWFLX4
Bio Rep 5, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Alignments (bam)
4DNFI3611HDO
234.13m
9.94%
15.995%
15.456%
0.001%
0.13%
Experiment
4DNEXEKL694J
Bio Rep 6, Tec Rep 1
Dilution Hi-C on IMR-90 with HindIII
File
Alignments (bam)
4DNFI72GPX3I
208.71m
9.49%
18.079%
21.704%
0.001%
0.128%