ExperimentSetReplicate

ExperimentSet4DNESTHQ7CR1
released
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Small-scale in situ Hi-C on mouse preimplantation embryos collected at PN3 zygotic stage and cultured in vitro for 20 h with alpha-amanitin

   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 
tissue
Sample 
embryo
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Enzyme: MboI

8 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESTHQ7CR1
Multiple Experiments
File
Contact List-combined (pairs)
4DNFITDL2BAJ
65.28m
54.115%
27.625%
18.26%
Experiment
4DNEXJFZUVEK
Bio Rep 1, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Contact List-replicate (pairs)
4DNFIRFTTY13
29.05m
60.808%
26.663%
12.529%
Experiment
4DNEXGABZ8RE
Bio Rep 2, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Contact List-replicate (pairs)
4DNFIXCPN625
36.23m
48.748%
28.396%
22.856%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESTHQ7CR1
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI7875Q16
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXJFZUVEK
Bio Rep 1, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Alignments (bam)
4DNFI77D8IIC
148.6m
9.781%
8.97%
38.06%
23.64%
0.184%
Experiment
4DNEXGABZ8RE
Bio Rep 2, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Alignments (bam)
4DNFITGDUBC1
150.56m
10.956%
9.633%
31.078%
24.269%
0.406%