ExperimentSetReplicate

ExperimentSet4DNESTHQ7CR1
released

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

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 
Biosource Type 
tissue
Biosource 
embryo
Experiment Type(s) 
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Enzyme: MboI

7 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
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%