ExperimentSetReplicate

ExperimentSet4DNESX8VOP7F
released
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HiChIP on trophoblast stem cells (TSC) from mouse

   December 4th, 2023 at 7:52pm
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

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
stem cells
Sample 
trophoblast cell
Experiment Type(s) 
HiChIP
Modification Type 
None
Treatment Type 
None
Assay Details 
Target: H3K27ac (mouse)

7 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESX8VOP7F
Multiple Experiments
File
Contact List-combined (pairs)
4DNFISNEAVYV
179.92m
45.637%
32.405%
21.959%
Experiment
4DNEX2ICGLRP
Bio Rep 1, Tec Rep 1
HiChIP against H3K27ac (mouse) on trophoblast cell
File
Contact List-replicate (pairs)
4DNFI6OUBGVU
90.34m
46.276%
34.11%
19.614%
Experiment
4DNEXOYEFWOB
Bio Rep 2, Tec Rep 1
HiChIP against H3K27ac (mouse) on trophoblast cell
File
Contact List-replicate (pairs)
4DNFIY17RMGV
89.58m
44.992%
30.685%
24.324%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESX8VOP7F
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIJ5K4FFQ
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX2ICGLRP
Bio Rep 1, Tec Rep 1
HiChIP against H3K27ac (mouse) on trophoblast cell
File
Alignments (bam)
4DNFIGCYJQPE
460.45m
7.141%
7.226%
48.969%
17.044%
0.039%
Experiment
4DNEXOYEFWOB
Bio Rep 2, Tec Rep 1
HiChIP against H3K27ac (mouse) on trophoblast cell
File
Alignments (bam)
4DNFIINWRQSC
481.31m
5.34%
8.864%
53.193%
13.99%
0.029%