ExperimentSetReplicate

ExperimentSet4DNESF17LNZE
released
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These are biological replicate in which we performed Liquid chromatin Hi-C on K652 cells. Nuclei were purified then were digested with DpnII for 4 hours before performing Hi-C 2.0

   June 4th, 2019 at 2:11pm
Source Publication
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.
Belaghzal H, Borrman T, et al., Nature genetics 2021

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
K562 (Tier 2)
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: DpnII

12 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESF17LNZE
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI7E8ENK6
601.97m
20.127%
13.808%
66.065%
Experiment
4DNEXN2CA8P8
Bio Rep 1, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Contact List-replicate (pairs)
4DNFIZUGLZ56
220m
20.289%
19.652%
60.059%
Experiment
4DNEXUB3SBP7
Bio Rep 2, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Contact List-replicate (pairs)
4DNFIG5GV21H
197.18m
20.73%
11.164%
68.106%
Experiment
4DNEXEK4WNHA
Bio Rep 3, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Contact List-replicate (pairs)
4DNFIK83V82Y
184.79m
19.292%
9.671%
71.038%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESF17LNZE
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIYW415LY
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXN2CA8P8
Bio Rep 1, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Alignments (bam)
4DNFIOU5IURE
537.73m
11.026%
12.987%
20.659%
14.416%
0.174%
Experiment
4DNEXUB3SBP7
Bio Rep 2, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Alignments (bam)
4DNFI3QVM9JZ
369.54m
8.207%
12.887%
16.348%
9.2%
0.25%
Experiment
4DNEXEK4WNHA
Bio Rep 3, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Alignments (bam)
4DNFI9JOOGOP
402.92m
12.238%
24.485%
17.409%
0.007%
0.164%