ExperimentSetReplicate

ExperimentSet4DNESXS1M9JR
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in situ Hi-C on E14Tg2 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 
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
4DNESXS1M9JR
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIYWZY5NC
367.78m
45.281%
42.491%
12.228%
Experiment
4DNEXGGI1YTN
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFIAN5BJNJ
177.52m
43.455%
44.605%
11.939%
Experiment
4DNEXO4M3JNS
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Contact List-replicate (pairs)
4DNFICZ8JTE4
190.26m
46.984%
40.519%
12.497%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESXS1M9JR
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIRIDQ4N3
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXGGI1YTN
Bio Rep 1, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFIBTVRQAZ
314.75m
7.978%
26.156%
9.461%
0.007%
0.135%
Experiment
4DNEXO4M3JNS
Bio Rep 2, Tec Rep 1
in situ Hi-C on ES-E14TG2a with DpnII
File
Alignments (bam)
4DNFIXUJI5H9
329.37m
7.38%
24.5%
10.348%
0.006%
0.099%