ExperimentSetReplicate

ExperimentSet4DNES3JWOSVS
released
View JSON

Small-scale in situ Hi-C on mouse PN3 zygotes

   January 10th, 2020 at 3:45pm
Source Publication
Allelic reprogramming of 3D chromatin architecture during early mammalian development.
Du Z, Zheng H, et al., Nature 2017

Assay Description  

Note on Processed Files  

Some annotated bam and pairs files generated in this Experiment Set may contain distinct reads that share the same identifier. This was caused by merging fastq files with integer identifiers (eg. @1, @2) during processing.

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
primary cells
Sample 
PN3 stage zygote
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MboI

10 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES3JWOSVS
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIS9JU5OD
104.95m
48.773%
31.419%
19.808%
Experiment
4DNEXGKGYCMK
Bio Rep 1, Tec Rep 1
in situ Hi-C on PN3 stage zygote with MboI
File
Contact List-replicate (pairs)
4DNFIEA4B3VN
63.31m
50.405%
31.107%
18.488%
Experiment
4DNEXQZR4G2T
Bio Rep 2, Tec Rep 1
in situ Hi-C on PN3 stage zygote with MboI
File
Contact List-replicate (pairs)
4DNFI8SPSSA3
41.64m
46.292%
31.894%
21.815%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES3JWOSVS
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIMU4OC9R
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXGKGYCMK
Bio Rep 1, Tec Rep 1
in situ Hi-C on PN3 stage zygote with MboI
File
Alignments (bam)
4DNFIDLCJQ4D
785.38m
45.223%
5.083%
23.755%
17.877%
0.115%
Experiment
4DNEXQZR4G2T
Bio Rep 2, Tec Rep 1
in situ Hi-C on PN3 stage zygote with MboI
File
Alignments (bam)
4DNFIFV91OE8
311.62m
11.053%
9.287%
41.813%
24.484%
0.268%