ExperimentSetReplicate

ExperimentSet4DNESGC3Z7E3
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in situ Hi-C on E14Tg2-dCas9 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
4DNESGC3Z7E3
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI1SBWYWV
361.2m
41.581%
47.811%
10.609%
Experiment
4DNEX4X3WHZC
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFIKSZDF51
175.73m
43.356%
46.136%
10.508%
Experiment
4DNEXYBNSCM1
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFIUPYNT42
185.47m
39.898%
49.397%
10.705%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESGC3Z7E3
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIF7DNLB6
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX4X3WHZC
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFIPOHMCL7
320.5m
7.966%
26.687%
10.509%
0.007%
0.143%
Experiment
4DNEXYBNSCM1
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFI443JG9O
322.22m
7.142%
25.133%
10.159%
0.007%
0.115%