ExperimentSetReplicate

ExperimentSet4DNESQT4SR5G
released
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in situ Hi-C on E14Tg2-dCas9VP64-p65 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 
  1. Stable Transfection
  2. 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
4DNESQT4SR5G
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIS4XRRW5
389.92m
39.717%
49.12%
11.163%
Experiment
4DNEX4K9CNZA
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFI79GYE71
199.97m
40.861%
46.533%
12.606%
Experiment
4DNEXKV5CP5B
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFIKWDX4BU
189.95m
38.513%
51.843%
9.644%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESQT4SR5G
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIFL7G5TM
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX4K9CNZA
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFIS9SSZC3
335.52m
6.976%
25.078%
8.339%
0.007%
0.104%
Experiment
4DNEXKV5CP5B
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFIKCKPXCJ
326.9m
8.058%
26.059%
7.769%
0.007%
0.14%