ExperimentSetReplicate

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ExperimentSet4DNESXWY8ILZ
released
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Hi-C on trophoblast stem cells (TSC) 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 
trophoblast cell
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: Arima - A1, A2

8 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
From Multiple Experiments
4DNESXWY8ILZ
Multiple Experiments
File
4DNFI9DUBGCW
contact list-combined (pairs)
997.33 MB
File
4DNFIIHXG8KW
contact matrix (hic)
1.04 GB
File
4DNFIOZ1TRUS
contact matrix (mcool)
659.19 MB
File
4DNFIDL82HOP
compartments (bw)
187.17 kB
Experiment
4DNEXCGCBZRQ
Bio Rep 1, Tec Rep 1
in situ Hi-C on trophoblast cell with Arima - A1, A2
File
4DNFIII8WENZ
alignments (bam)
4.61 GB
File
4DNFI9963UBE
contact list-replicate (pairs)
519.65 MB
Experiment
4DNEXXEDFFPL
Bio Rep 2, Tec Rep 1
in situ Hi-C on trophoblast cell with Arima - A1, A2
File
4DNFIXZVERSH
alignments (bam)
4.51 GB
File
4DNFI88AW2XK
contact list-replicate (pairs)
505.85 MB

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESXWY8ILZ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI9DUBGCW
68.63m
57.902%
19.947%
22.151%
Experiment
4DNEXCGCBZRQ
Bio Rep 1, Tec Rep 1
in situ Hi-C on trophoblast cell with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFI9963UBE
34.79m
57.905%
19.96%
22.135%
Experiment
4DNEXXEDFFPL
Bio Rep 2, Tec Rep 1
in situ Hi-C on trophoblast cell with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFI88AW2XK
33.84m
57.899%
19.935%
22.166%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESXWY8ILZ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIOZ1TRUS
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXCGCBZRQ
Bio Rep 1, Tec Rep 1
in situ Hi-C on trophoblast cell with Arima - A1, A2
File
Alignments (bam)
4DNFIII8WENZ
58m
14.132%
22.087%
3.718%
0.09%
0.074%
Experiment
4DNEXXEDFFPL
Bio Rep 2, Tec Rep 1
in situ Hi-C on trophoblast cell with Arima - A1, A2
File
Alignments (bam)
4DNFIXZVERSH
56.83m
14.482%
22.008%
3.864%
0.09%
0.074%