ExperimentSetReplicate

ExperimentSet4DNES6U3U9PJ
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

   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 
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
4DNES6U3U9PJ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI7LOZQQW
149.18m
56.289%
24.866%
18.844%
Experiment
4DNEXK4N86S8
Bio Rep 1, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Contact List-replicate (pairs)
4DNFIAX6VMMX
96.49m
57.125%
23.986%
18.889%
Experiment
4DNEXBC7DJFL
Bio Rep 2, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Contact List-replicate (pairs)
4DNFIGRY4UZQ
52.69m
54.76%
26.478%
18.762%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES6U3U9PJ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFILBV6VDS
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXK4N86S8
Bio Rep 1, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Alignments (bam)
4DNFI9LWZTLP
326.55m
10.394%
8.737%
28.174%
23.145%
0.146%
Experiment
4DNEXBC7DJFL
Bio Rep 2, Tec Rep 1
in situ Hi-C on embryo with MboI
File
Alignments (bam)
4DNFI5EYO8UT
225.81m
27.07%
6.733%
22.144%
20.721%
0.07%