ExperimentSetReplicate

ExperimentSet4DNESCE6QH8A
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Hi-C on extra embryonic stem cells (XEN) from mouse

   December 4th, 2023 at 7:48pm
Source Publication
Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression.
Murphy D, Salataj E, et al., bioRxiv : the preprint server for biology 2023

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
stem cells
Sample 
extraembryonic cell
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: Arima - A1, A2

10 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESCE6QH8A
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIJSRR3NO
199.98m
56.76%
26.141%
17.099%
Experiment
4DNEX1WDJN31
Bio Rep 1, Tec Rep 1
in situ Hi-C on extraembryonic cell with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFIF6V5PUA
95.84m
55.682%
26.997%
17.321%
Experiment
4DNEXGW42CPK
Bio Rep 2, Tec Rep 1
in situ Hi-C on extraembryonic cell with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFIE2K6SPR
104.14m
57.752%
25.353%
16.895%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESCE6QH8A
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIA3UO9AC
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX1WDJN31
Bio Rep 1, Tec Rep 1
in situ Hi-C on extraembryonic cell with Arima - A1, A2
File
Alignments (bam)
4DNFIAV1G95X
171.18m
16.124%
21.146%
6.68%
0.062%
0.096%
Experiment
4DNEXGW42CPK
Bio Rep 2, Tec Rep 1
in situ Hi-C on extraembryonic cell with Arima - A1, A2
File
Alignments (bam)
4DNFIQ6NFWCU
175.59m
11.548%
22.313%
6.759%
0.073%
0.111%