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ExperimentSet4DNESG53SEUU
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Multiplexed FISH in Sox2 tagged mouse embryonic stem cell line (F123-CASTx129) with a 7.5kb insertion containing 4 CTCF binding sites introduced between Sox2 and its Super Enhancer, in 24hrs differentiation media.

   February 3rd, 2025 at 3:47pm
Source Publication
Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery.
Tastemel M, Jussila A, et al., bioRxiv : the preprint server for biology 2025

Data Usage Guidelines  

Data Use Guidelines: This is a data set generated by the 4DN Network and made freely available to the scientific community. If you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper (doi:10.1038/nature23884) and the 4DN Data Portal paper (doi:10.1038/s41467-022-29697-4), and please acknowledge the 4DN lab which generated the data. Please direct any questions to the Data Coordination and Integration Center.

Note on FOF-CT file format  

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
stem cells
Sample 
F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE
Experiment Type(s) 
multiplexed FISH
Modification Type 
Crispr
Treatment Type 
None
Assay Details 
Target: 101 40-bp regions on Chr11 (mouse), 4470 40-bp on the 205kb stretch from Sox2 gene to SE and surrounding regions (mouse), Chromosomes
Channel
Imaging Rounds
Path
 
ch00
1
DAPI staining
ch03
1
101 40-bp regions on Chr11 (mouse) placed as a 7.5kb insertion between Sox2 promoter and SE, targeted by Alexa Fluor 647 (Imaging probes)
ch01
2-15
4470 40-bp on the 205kb stretch from Sox2 gene to SE and surrounding regions (mouse) targeted by Fluospheres 505 (Fiducial probes)
ch02
2-15
4470 40-bp on the 205kb stretch from Sox2 gene to SE and surrounding regions (mouse) targeted by Alexa Fluor 750 (Imaging probes)
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1 Processed File

Experiment
File
File Type
File Size
Experiment
4DNEX9XXD7C8
Bio Rep 1, Tec Rep 1
multiplexed FISH on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE
File
4DNFILU5QBU3
FOF-CT - DNA-spot/trace core (csv)
4.94 MB