ExperimentSetReplicate

ExperimentSet4DNES3Y26CEU
released
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in situ Hi-C on E14Tg2-dCas9VP64 cell line infected by zfp608 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
4DNES3Y26CEU
Multiple Experiments
File
Contact List-combined (pairs)
4DNFICVHDPBF
377.15m
51.459%
35.542%
12.999%
Experiment
4DNEXTJ6TT4G
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFIGO2YI71
189.57m
58.473%
28.099%
13.428%
Experiment
4DNEXWLVASKX
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFI4DBSNQ6
187.59m
44.372%
43.063%
12.565%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES3Y26CEU
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIBGXE6F6
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXTJ6TT4G
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFI5ZXTA5X
326.82m
7.668%
24.36%
9.964%
0.005%
0.1%
Experiment
4DNEXWLVASKX
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFIFR62R5P
317.07m
7.326%
24.211%
9.294%
0.007%
0.109%