ExperimentSetReplicate

ExperimentSet4DNESFLV3UMN
released
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In situ Hi-C with DdeI on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) 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 
in vitro differentiated cells
Sample 
H1-hESC differentiated to definitive endoderm
Experiment Type(s) 
in situ Hi-C
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
From Multiple Experiments
4DNESFLV3UMN
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI6VQO96P
162.26m
36.551%
43.139%
20.309%
Experiment
4DNEXW481RNF
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC differentiated to definitive endoderm with DdeI
File
Contact List-replicate (pairs)
4DNFIW6FMQKJ
162.26m
36.551%
43.139%
20.309%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESFLV3UMN
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI3724MS8
None
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
File
Alignments (bam)
4DNFIJG9B5DV
365.14m
15.17%
18.882%
21.504%
0.005%
0.062%