ExperimentSetReplicate

ExperimentSet4DNESBBYGJFA
released
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in situ Hi-C on E14Tg2 cell line infected by sox4 gRNA

   August 12th, 2019 at 2:59pm
Source Publication
Multiscale 3D Genome Rewiring during Mouse Neural Development.
Bonev B, Mendelson Cohen N, et al., Cell 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 
stem cells
Sample 
ES-E14TG2a
Experiment Type(s) 
in situ Hi-C
Modification Type 
Crispr
Treatment Type 
None
Assay Details 
Enzyme: DpnII

10 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESBBYGJFA
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIXF2H1CW
396.19m
40.303%
48.176%
11.521%
Experiment
4DNEXEIHUOMJ
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFIHZLQGQV
199.69m
35.424%
53.761%
10.815%
Experiment
4DNEXIUM9BKI
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFIXUPMKU7
196.51m
45.26%
42.501%
12.239%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESBBYGJFA
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI17N23FN
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXEIHUOMJ
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFI3C4S1EY
358.66m
6.645%
25.43%
12.242%
0.008%
0.108%
Experiment
4DNEXIUM9BKI
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFI1QABQSJ
331.7m
7.784%
25.049%
7.916%
0.007%
0.152%