ExperimentSetReplicate

ExperimentSet4DNESUQT299T
released
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Small-scale in situ Hi-C on mouse cortex

   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 
cerebral cortex
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
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
4DNESUQT299T
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIZ51VHLF
61.98m
55.572%
27.037%
17.391%
Experiment
4DNEXT1SU5GQ
Bio Rep 1, Tec Rep 1
in situ Hi-C on cerebral cortex with MboI
File
Contact List-replicate (pairs)
4DNFIA8HVQYQ
28.92m
55.738%
26.83%
17.432%
Experiment
4DNEXNCQS8V9
Bio Rep 2, Tec Rep 1
in situ Hi-C on cerebral cortex with MboI
File
Contact List-replicate (pairs)
4DNFIQW9S38C
33.06m
55.427%
27.218%
17.355%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESUQT299T
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI2H23JBK
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXT1SU5GQ
Bio Rep 1, Tec Rep 1
in situ Hi-C on cerebral cortex with MboI
File
Alignments (bam)
4DNFI37OJQV2
46.92m
11.047%
14.423%
2.203%
10.694%
0.122%
Experiment
4DNEXNCQS8V9
Bio Rep 2, Tec Rep 1
in situ Hi-C on cerebral cortex with MboI
File
Alignments (bam)
4DNFI2GRYFG5
53.72m
11.072%
13.804%
2.567%
11.014%
0.093%