ExperimentSetReplicate

Browser Suggestion

Google Chrome  or Mozilla Firefox are the recommended browser(s) for using the 4DN Data Portal.

Microsoft Edge, Safari, Opera etc. should work for a majority of portal functions but are not explicitly supported and may present some glitches, e.g. during submission.

ExperimentSet4DNESPPSOUKK
released
View JSON

Micro-C on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) 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

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) 
Micro-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MNase

8 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
From Multiple Experiments
4DNESPPSOUKK
Multiple Experiments
File
4DNFI2L94L23
contact list-combined (pairs)
2.5 GB
File
4DNFI59Y6R69
contact matrix (hic)
1.73 GB
File
4DNFII4IPDTR
contact matrix (mcool)
1.04 GB
File
4DNFIZMP8TXH
boundaries (bed)
232.07 kB
File
4DNFI6847LX6
insulation score-diamond (bw)
8.02 MB
File
4DNFI1RZIGGI
compartments (bw)
205.85 kB
Experiment
4DNEXVCM43FD
Bio Rep 1, Tec Rep 1
Micro-C on H1-hESC differentiated to definitive endoderm with MNase
File
4DNFIK42NPWU
alignments (bam)
26.18 GB
File
4DNFIH5T6EB8
contact list-replicate (pairs)
2.5 GB

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESPPSOUKK
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI2L94L23
138.14m
25.67%
42.214%
32.115%
Experiment
4DNEXVCM43FD
Bio Rep 1, Tec Rep 1
Micro-C on H1-hESC differentiated to definitive endoderm with MNase
File
Contact List-replicate (pairs)
4DNFIH5T6EB8
138.14m
25.67%
42.214%
32.115%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESPPSOUKK
Multiple Experiments
File
Contact Matrix (mcool)
4DNFII4IPDTR
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXVCM43FD
Bio Rep 1, Tec Rep 1
Micro-C on H1-hESC differentiated to definitive endoderm with MNase
File
Alignments (bam)
4DNFIK42NPWU
355.14m
6.65%
17.237%
37.209%
0.006%
0.091%