ExperimentSetReplicate

ExperimentSet4DNESXZHIUAU
released
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Small-scale in situ Hi-C on mouse late 2-cell embryos

   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 
Late 2-cell stage embryo
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
4DNESXZHIUAU
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIFLS1BSB
274.69m
46.932%
28.169%
24.9%
Experiment
4DNEXOSG8OXE
Bio Rep 1, Tec Rep 1
in situ Hi-C on Late 2-cell stage embryo with MboI
File
Contact List-replicate (pairs)
4DNFIPLGJJ91
58.75m
49.639%
28.85%
21.511%
Experiment
4DNEXM5XEQNN
Bio Rep 2, Tec Rep 1
in situ Hi-C on Late 2-cell stage embryo with MboI
File
Contact List-replicate (pairs)
4DNFI1JB7E6J
51.32m
47.568%
27.592%
24.84%
Experiment
4DNEX4U1GKC1
Bio Rep 3, Tec Rep 1
in situ Hi-C on Late 2-cell stage embryo with MboI
File
Contact List-replicate (pairs)
4DNFIU7DL977
83.52m
40.783%
24.449%
34.768%
Experiment
4DNEXHFCMUAI
Bio Rep 4, Tec Rep 1
in situ Hi-C on Late 2-cell stage embryo with MboI
File
Contact List-replicate (pairs)
4DNFILEFNUZY
81.1m
50.9%
31.871%
17.229%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESXZHIUAU
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIIWW8LIF
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXOSG8OXE
Bio Rep 1, Tec Rep 1
in situ Hi-C on Late 2-cell stage embryo with MboI
File
Alignments (bam)
4DNFIUYJ9D9E
302.47m
29.349%
8.053%
28.766%
14.409%
0.108%
Experiment
4DNEXM5XEQNN
Bio Rep 2, Tec Rep 1
in situ Hi-C on Late 2-cell stage embryo with MboI
File
Alignments (bam)
4DNFIPJAHZEC
224.13m
11.696%
8.715%
30.847%
25.845%
0.261%
Experiment
4DNEX4U1GKC1
Bio Rep 3, Tec Rep 1
in situ Hi-C on Late 2-cell stage embryo with MboI
File
Alignments (bam)
4DNFIJXGHTZO
327.49m
9.857%
9.308%
33.805%
21.527%
0.156%
Experiment
4DNEXHFCMUAI
Bio Rep 4, Tec Rep 1
in situ Hi-C on Late 2-cell stage embryo with MboI
File
Alignments (bam)
4DNFIUJUQLZR
239.75m
10.158%
9.602%
24.556%
21.859%
0.476%