ExperimentSetReplicate

ExperimentSet4DNESLTRW5KE
released
View JSON

In situ Hi-C with DpnII on H1 embryonic stem cells from Maehr lab 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 
stem cells
Sample 
H1-hESC
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
4DNESLTRW5KE
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIK8ZDQR8
169.65m
35.416%
36.346%
28.238%
Experiment
4DNEXW32FN59
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC with DpnII
File
Contact List-replicate (pairs)
4DNFIEI1KDCU
169.65m
35.416%
36.346%
28.238%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESLTRW5KE
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIOEYIQ7R
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXW32FN59
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC with DpnII
File
Alignments (bam)
4DNFIQYG1SAM
371.93m
17.266%
22.473%
14.643%
0.006%
0.055%