ExperimentSetReplicate

ExperimentSet4DNESTXE7D88
released
View JSON

In situ Hi-C with HindIII on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde and 3mM DSG 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: HindIII

8 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESTXE7D88
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI2KO91DH
223.23m
39.149%
31.776%
29.075%
Experiment
4DNEXYOKS2Q9
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC differentiated to definitive endoderm with HindIII
File
Contact List-replicate (pairs)
4DNFIZZGEMCX
223.23m
39.149%
31.776%
29.075%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESTXE7D88
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIJ8GSITT
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXYOKS2Q9
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC differentiated to definitive endoderm with HindIII
File
Alignments (bam)
4DNFIJDQEXFQ
378.02m
15.131%
12.837%
12.973%
0.007%
0.093%