ExperimentSetReplicate

ExperimentSet4DNES68MSHVU
released

in situ Hi-C on E14Tg2-dCas9 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 
Sample Type 
stem cells
Sample 
Experiment Type(s) 
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
4DNES68MSHVU
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIM4EYR7Z
398.83m
39.383%
49.459%
11.158%
Experiment
4DNEXUIOAGJ7
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFIVPQYGQU
194.87m
32.731%
57.567%
9.702%
Experiment
4DNEX5O7D76E
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFIZGW1QQA
203.96m
45.738%
41.713%
12.549%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES68MSHVU
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIQEYBCFU
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXUIOAGJ7
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFIKFVZEDB
343.73m
6.728%
25.775%
10.797%
0.007%
0.11%
Experiment
4DNEX5O7D76E
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFIUOPQCGH
338.1m
7.665%
24.633%
7.37%
0.007%
0.144%