ExperimentSetReplicate

ExperimentSet4DNESNIUM3LC
released
View JSON

In situ Hi-C with DpnII on HFF cells with 1% Formaldehyde and 3mM EGS crosslinking

   June 27th, 2020 at 6:56pm
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 
HFF-hTERT
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: DpnII

8 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESNIUM3LC
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIKVL3ZUR
202.48m
51.839%
25.737%
22.423%
Experiment
4DNEXDX613HH
Bio Rep 1, Tec Rep 1
in situ Hi-C on HFF-hTERT with DpnII
File
Contact List-replicate (pairs)
4DNFI2N7JJN7
202.48m
51.839%
25.737%
22.423%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESNIUM3LC
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIBRZPWTF
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXDX613HH
Bio Rep 1, Tec Rep 1
in situ Hi-C on HFF-hTERT with DpnII
File
Alignments (bam)
4DNFI9Y8L5DB
372.45m
12.753%
21.752%
11.126%
0.004%
0.109%