ExperimentSet4DNESFLV3UMN
released
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: DdeI
8 Processed Files
Quality Metrics
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
Experiment
4DNEXW481RNF
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC differentiated to definitive endoderm with DdeIExperiment
For File
Failed Balancing
Details
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXW481RNF
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC differentiated to definitive endoderm with DdeI