ExperimentSetReplicate

ExperimentSet4DNESJ9SIAV5
released
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in situ Hi-C on in-vitro differentiated mouse neural progenitors cells 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  

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
in vitro differentiated cells
Sample 
46C with Sox1-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
4DNESJ9SIAV5
Multiple Experiments
File
Contact List-combined (pairs)
4DNFINF11PQS
5.37 billion
52.478%
19.494%
28.028%
Experiment
4DNEXOPQXJ3G
Bio Rep 1, Tec Rep 1
in situ Hi-C on 46C with Sox1-GFP with DpnII
File
Contact List-replicate (pairs)
4DNFIEB68WXR
833.25m
59.066%
18.02%
22.914%
Experiment
4DNEXNPE4ZEU
Bio Rep 2, Tec Rep 1
in situ Hi-C on 46C with Sox1-GFP with DpnII
File
Contact List-replicate (pairs)
4DNFISOG5MP4
1.32 billion
48.44%
20.09%
31.47%
Experiment
4DNEXVBF7QRA
Bio Rep 3, Tec Rep 1
in situ Hi-C on 46C with Sox1-GFP with DpnII
File
Contact List-replicate (pairs)
4DNFICX5IXBH
926.76m
46.683%
28.309%
25.008%
Experiment
4DNEXYY2LOHJ
Bio Rep 4, Tec Rep 1
in situ Hi-C on 46C with Sox1-GFP with DpnII
File
Contact List-replicate (pairs)
4DNFIIE6F9N5
2.29 billion
54.756%
16.118%
29.126%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESJ9SIAV5
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIKK3QG34
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXOPQXJ3G
Bio Rep 1, Tec Rep 1
in situ Hi-C on 46C with Sox1-GFP with DpnII
File
Alignments (bam)
4DNFIM5GJ1AI
1.28 billion
7.503%
23.745%
3.896%
0.003%
0.064%
Experiment
4DNEXNPE4ZEU
Bio Rep 2, Tec Rep 1
in situ Hi-C on 46C with Sox1-GFP with DpnII
File
Alignments (bam)
4DNFI7W3KOFC
2.18 billion
6.547%
25.593%
7.387%
0.003%
0.071%
Experiment
4DNEXVBF7QRA
Bio Rep 3, Tec Rep 1
in situ Hi-C on 46C with Sox1-GFP with DpnII
File
Alignments (bam)
4DNFIE7VJPO3
1.54 billion
6.96%
27.481%
5.557%
0.003%
0.075%
Experiment
4DNEXYY2LOHJ
Bio Rep 4, Tec Rep 1
in situ Hi-C on 46C with Sox1-GFP with DpnII
File
Alignments (bam)
4DNFIQ44UGEL
3.71 billion
6.781%
24.256%
7.235%
0.003%
0.067%