ExperimentSetReplicate

ExperimentSet4DNESDXUWBD9
released
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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 
M. musculus
Sample Type 
stem cells
Sample 
mESC line with Oct4-GFP
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: DpnII

14 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
Failed Balancing
Details
From Multiple Experiments
4DNESDXUWBD9
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIC21MG3U
None
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%