ExperimentSetReplicate

ExperimentSet4DNESEDV9YMX
released
View JSON

In situ Hi-C with HindIII on HeLa-S3 (mitotic) 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 
H. sapiens
Sample Type 
immortalized cells
Sample 
HeLa-S3
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
Chemical
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
4DNESEDV9YMX
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIABHXPJ5
198.35m
76.79%
16.87%
6.34%
Experiment
4DNEXR3L8DZL
Bio Rep 1, Tec Rep 1
in situ Hi-C on HeLa-S3 with HindIII
File
Contact List-replicate (pairs)
4DNFIZHGYENC
198.35m
76.79%
16.87%
6.34%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESEDV9YMX
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI9P5JY7X
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXR3L8DZL
Bio Rep 1, Tec Rep 1
in situ Hi-C on HeLa-S3 with HindIII
File
Alignments (bam)
4DNFI46T8M7U
379.61m
12.392%
14.524%
20.829%
0.003%
0.057%