ExperimentSetReplicate

ExperimentSet4DNESDBUUEL9
released
View JSON

In situ Hi-C with DdeI on HFF cells with 1% Formaldehyde and 3mM DSG 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: DdeI

8 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESDBUUEL9
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIIHQPL9U
212.16m
52.831%
25.167%
22.003%
Experiment
4DNEX4A7XMOY
Bio Rep 1, Tec Rep 1
in situ Hi-C on HFF-hTERT with DdeI
File
Contact List-replicate (pairs)
4DNFIVFLHG38
212.16m
52.831%
25.167%
22.003%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESDBUUEL9
Multiple Experiments
File
Contact Matrix (mcool)
4DNFILCOOE2K
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX4A7XMOY
Bio Rep 1, Tec Rep 1
in situ Hi-C on HFF-hTERT with DdeI
File
Alignments (bam)
4DNFIYGKO8OZ
379.91m
11.877%
18.68%
13.594%
0.004%
0.109%