ExperimentSetReplicate

ExperimentSet4DNESSH9ICEW
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 16 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

10 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESSH9ICEW
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI7ARIWZ1
407.43m
10.513%
9.06%
80.427%
Experiment
4DNEXNTNUKJY
Bio Rep 1, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Contact List-replicate (pairs)
4DNFIKLVEOBB
207.04m
9.397%
8.492%
82.111%
Experiment
4DNEXLSBD323
Bio Rep 2, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Contact List-replicate (pairs)
4DNFI8ZAC4LD
200.39m
11.666%
9.647%
78.687%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESSH9ICEW
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIZ3ME9L5
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXNTNUKJY
Bio Rep 1, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Alignments (bam)
4DNFITQOXHR4
345.94m
7.298%
13.301%
10.975%
8.577%
0.315%
Experiment
4DNEXLSBD323
Bio Rep 2, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Alignments (bam)
4DNFIPGNU916
397.22m
12.039%
24.249%
13.257%
0.006%
0.192%