ExperimentSetReplicate

ExperimentSet4DNES1J8MC4Q
released
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Small-scale in situ Hi-C on mouse PN5 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 
PN5 stage zygote
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MboI

14 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES1J8MC4Q
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIZ59RT2J
198.61m
47.335%
31.033%
21.633%
Experiment
4DNEXXZOPUC2
Bio Rep 1, Tec Rep 1
in situ Hi-C on PN5 stage zygote with MboI
File
Contact List-replicate (pairs)
4DNFI3JD3XNX
55.62m
50.301%
31.222%
18.477%
Experiment
4DNEX2JFIA1O
Bio Rep 2, Tec Rep 1
in situ Hi-C on PN5 stage zygote with MboI
File
Contact List-replicate (pairs)
4DNFI4T1IM11
45.92m
47.973%
31.21%
20.818%
Experiment
4DNEXE5F6RB4
Bio Rep 3, Tec Rep 1
in situ Hi-C on PN5 stage zygote with MboI
File
Contact List-replicate (pairs)
4DNFITQXLWSM
44.5m
45.755%
30.41%
23.835%
Experiment
4DNEX2FFAUYV
Bio Rep 4, Tec Rep 1
in situ Hi-C on PN5 stage zygote with MboI
File
Contact List-replicate (pairs)
4DNFIS45KZF6
52.57m
44.976%
31.204%
23.82%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES1J8MC4Q
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIDFYUWC3
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXXZOPUC2
Bio Rep 1, Tec Rep 1
in situ Hi-C on PN5 stage zygote with MboI
File
Alignments (bam)
4DNFIHRC63BD
456.04m
11.295%
10.006%
46.357%
20.146%
0.35%
Experiment
4DNEX2JFIA1O
Bio Rep 2, Tec Rep 1
in situ Hi-C on PN5 stage zygote with MboI
File
Alignments (bam)
4DNFIEHCGLJE
284.37m
8.846%
10.194%
46.705%
18.106%
0.339%
Experiment
4DNEXE5F6RB4
Bio Rep 3, Tec Rep 1
in situ Hi-C on PN5 stage zygote with MboI
File
Alignments (bam)
4DNFIHYAY2FP
259.42m
9.933%
9.032%
41.98%
21.899%
0.197%
Experiment
4DNEX2FFAUYV
Bio Rep 4, Tec Rep 1
in situ Hi-C on PN5 stage zygote with MboI
File
Alignments (bam)
4DNFIQXWNQ1T
390.26m
9.655%
9.559%
44.23%
23.085%
0.243%