ExperimentSetReplicate

ExperimentSet4DNESV4MND3G
released
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In situ Hi-C with DdeI on H1 embryonic stem cells from Maehr lab 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

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: DdeI

8 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESV4MND3G
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI731KGWC
175.43m
36.563%
27.036%
36.401%
Experiment
4DNEXRAUHVDK
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC with DdeI
File
Contact List-replicate (pairs)
4DNFIE2ORUCS
175.43m
36.563%
27.036%
36.401%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESV4MND3G
Multiple Experiments
File
Contact Matrix (mcool)
4DNFII2G4NT7
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXRAUHVDK
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC with DdeI
File
Alignments (bam)
4DNFIX11U3RK
353.53m
14.504%
19.524%
16.338%
0.013%
0.349%