ExperimentSetReplicate

ExperimentSet4DNESDXUWBD9
released

in situ Hi-C on mouse embryonic stem cell GFP+ and G0G1 FACS sorted

   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 
Biosource Type 
stem cell derived cell line
Biosource 
mESC line with Oct4-GFP
Experiment Type(s) 
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: DpnII

11 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESDXUWBD9
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI9MU6OR9
4.26 billion
49.579%
35.685%
14.736%
Experiment
4DNEXRQ75YRG
Bio Rep 1, Tec Rep 1
in situ Hi-C on mESC line with Oct4-GFP with DpnII
File
Contact List-replicate (pairs)
4DNFIDL76RBL
1.47 billion
53.274%
32.563%
14.163%
Experiment
4DNEXQDT453K
Bio Rep 2, Tec Rep 1
in situ Hi-C on mESC line with Oct4-GFP with DpnII
File
Contact List-replicate (pairs)
4DNFI9FPCAC7
785.4m
47.201%
40.114%
12.685%
Experiment
4DNEX31J4Q7Y
Bio Rep 3, Tec Rep 1
in situ Hi-C on mESC line with Oct4-GFP with DpnII
File
Contact List-replicate (pairs)
4DNFI9E5ET4Q
1.68 billion
48.557%
34.74%
16.703%
Experiment
4DNEXNL1VDH7
Bio Rep 4, Tec Rep 1
in situ Hi-C on mESC line with Oct4-GFP with DpnII
File
Contact List-replicate (pairs)
4DNFI1JJ4AOW
324.99m
43.879%
43.975%
12.146%
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXRQ75YRG
Bio Rep 1, Tec Rep 1
in situ Hi-C on mESC line with Oct4-GFP with DpnII
File
Alignments (bam)
4DNFIP58NC51
2.58 billion
7.582%
23.407%
12.126%
0.003%
0.061%
Experiment
4DNEXQDT453K
Bio Rep 2, Tec Rep 1
in situ Hi-C on mESC line with Oct4-GFP with DpnII
File
Alignments (bam)
4DNFI8JW5ZOR
1.33 billion
6.752%
23.555%
10.501%
0.003%
0.071%
Experiment
4DNEX31J4Q7Y
Bio Rep 3, Tec Rep 1
in situ Hi-C on mESC line with Oct4-GFP with DpnII
File
Alignments (bam)
4DNFIQN4TCLV
2.81 billion
6.266%
24.236%
9.929%
0.003%
0.079%
Experiment
4DNEXNL1VDH7
Bio Rep 4, Tec Rep 1
in situ Hi-C on mESC line with Oct4-GFP with DpnII
File
Alignments (bam)
4DNFIKNJJAKV
536.27m
6.112%
23.746%
9.537%
0.003%
0.071%