ExperimentSetReplicate

ExperimentSet4DNESN49VY8X
released
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Hi-C experiments on HFFc6 crosslinked with both FA and DSG, digested with DdeI and DpnII.

   June 24th, 2020 at 8:17pm
Source Publication
Systematic evaluation of chromosome conformation capture assays.
Akgol Oksuz B, Yang L, et al., Nature methods 2021

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
HFFc6 (Tier 1)
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: DdeI and DpnII

10 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESN49VY8X
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIYIDJIBN
3.2 billion
40.39%
48.817%
10.793%
Experiment
4DNEXDL7KBH2
Bio Rep 1, Tec Rep 1
in situ Hi-C on HFFc6 (Tier 1) with DdeI and DpnII
File
Contact List-replicate (pairs)
4DNFIOFGGOP6
1.67 billion
39.491%
50.101%
10.408%
Experiment
4DNEXSFVDRQD
Bio Rep 2, Tec Rep 1
in situ Hi-C on HFFc6 (Tier 1) with DdeI and DpnII
File
Contact List-replicate (pairs)
4DNFI57GU23E
1.53 billion
41.374%
47.41%
11.215%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESN49VY8X
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI8ZYY7VT
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXDL7KBH2
Bio Rep 1, Tec Rep 1
in situ Hi-C on HFFc6 (Tier 1) with DdeI and DpnII
File
Alignments (bam)
4DNFIRWVMHBY
3.31 billion
14.04%
21.477%
13.93%
0.011%
0.06%
Experiment
4DNEXSFVDRQD
Bio Rep 2, Tec Rep 1
in situ Hi-C on HFFc6 (Tier 1) with DdeI and DpnII
File
Alignments (bam)
4DNFIJHPI8M8
3.28 billion
14.682%
21.19%
17.573%
0.009%
0.054%