ExperimentSetReplicate

ExperimentSet4DNES6VNJ14M
released

In situ Hi-C with HindIII on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde 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

WARNING: non-optimal cross-linking conditions  


This dataset may be obtained with non-optimal cross-linking conditions (as demonstrated in the paper) and is reported here for documentation purposes.

Users interested in using Hi-C or Micro-C data from this project for alternative analyses are advised to use only datasets generated with the optimal cross-linking conditions of 1% Formaldehyde + 3mM DSG. The study authors further advise users to carefully select digestion enzymes and library size to fit their needs. A list of preferred datasets for re-use is provided.

Assay Description  



Experiment Set Properties  


Set Type 
Replicate
Organism 
Sample Type 
in vitro differentiated cells
Experiment Type(s) 
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: HindIII

8 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES6VNJ14M
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIGTIJTHQ
206.26m
44.82%
19.598%
35.582%
File
Contact List-replicate (pairs)
4DNFIE1YH8VL
206.26m
44.82%
19.598%
35.582%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES6VNJ14M
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIZTQKBMM
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
File
Alignments (bam)
4DNFILKMZCT1
379.07m
12.553%
15.21%
17.824%
0.002%
0.085%