ExperimentSetReplicate

ExperimentSet4DNES7RYT7KA
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 45 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
4DNES7RYT7KA
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIHQVAYDM
62.58m
56.48%
26.565%
16.955%
Experiment
4DNEXYIMVXHT
Bio Rep 1, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Contact List-replicate (pairs)
4DNFIK5JY283
31.93m
59.169%
26.405%
14.427%
Experiment
4DNEX9IOW37P
Bio Rep 2, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Contact List-replicate (pairs)
4DNFIJFSJMRQ
30.65m
53.68%
26.733%
19.588%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES7RYT7KA
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIDIZMP9E
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXYIMVXHT
Bio Rep 1, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Alignments (bam)
4DNFIMUTU3RI
165.5m
10.234%
8.967%
37.498%
24.009%
0.181%
Experiment
4DNEX9IOW37P
Bio Rep 2, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Alignments (bam)
4DNFIQIDEBXC
154.99m
11.501%
9.686%
35.776%
23.26%
0.327%