ExperimentSetReplicate

ExperimentSet4DNESQV6Y4JL
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 incubated with just digestion buffer 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
4DNESQV6Y4JL
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI7HCPDIT
460.01m
40.511%
18.699%
40.79%
Experiment
4DNEXTUFGQTJ
Bio Rep 1, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Contact List-replicate (pairs)
4DNFIXLRBJSK
285.64m
40.635%
22.749%
36.616%
Experiment
4DNEXN17DXV8
Bio Rep 2, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Contact List-replicate (pairs)
4DNFIW66CMJY
145.77m
40.352%
11.85%
47.798%
Experiment
4DNEXFE37TA2
Bio Rep 3, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Contact List-replicate (pairs)
4DNFI5IM9VWA
28.6m
40.079%
13.154%
46.767%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESQV6Y4JL
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIZT8DRA6
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXTUFGQTJ
Bio Rep 1, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Alignments (bam)
4DNFIO57FUOI
630.17m
12.461%
12.068%
18.514%
11.629%
0.142%
Experiment
4DNEXN17DXV8
Bio Rep 2, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Alignments (bam)
4DNFIS9LMTA6
356.47m
7.879%
12.84%
29.184%
9.206%
0.169%
Experiment
4DNEXFE37TA2
Bio Rep 3, Tec Rep 1
in situ Hi-C on K562 (Tier 2) with DpnII
File
Alignments (bam)
4DNFIPVSMV4U
53.34m
12.883%
24.288%
9.204%
0.007%
0.152%