ExperimentSetReplicate

ExperimentSet4DNESTTX579P
released
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In situ Hi-C with HindIII 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

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 
stem cells
Sample 
H1-hESC
Experiment Type(s) 
in situ Hi-C
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
4DNESTTX579P
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIZTCXQV9
219.81m
39.686%
32.665%
27.649%
Experiment
4DNEX83C4KR6
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC with HindIII
File
Contact List-replicate (pairs)
4DNFIQTBNLN1
219.81m
39.686%
32.665%
27.649%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESTTX579P
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIOJJCGMD
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX83C4KR6
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC with HindIII
File
Alignments (bam)
4DNFIZHHO5SV
374.07m
16.371%
12.383%
12.479%
0.006%
0.075%