ExperimentSetReplicate

ExperimentSet4DNESQICH2XW
released
View JSON

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: HindIII

10 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESQICH2XW
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIXKPOGGK
517.77m
19.005%
17.379%
63.615%
Experiment
4DNEXXHQLZJS
Bio Rep 1, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with HindIII
File
Contact List-replicate (pairs)
4DNFI1I34WQ2
214.18m
21.018%
16.182%
62.8%
Experiment
4DNEXQP66GOS
Bio Rep 2, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with HindIII
File
Contact List-replicate (pairs)
4DNFISZ17W81
303.58m
17.585%
18.224%
64.191%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESQICH2XW
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIMIYU8VC
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXXHQLZJS
Bio Rep 1, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with HindIII
File
Alignments (bam)
4DNFIBGYJPXD
336.37m
14.294%
20.095%
1.933%
0.003%
0.178%
Experiment
4DNEXQP66GOS
Bio Rep 2, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with HindIII
File
Alignments (bam)
4DNFIODP573E
623.6m
13.144%
21.327%
16.834%
0.013%
0.174%