ExperimentSetReplicate

ExperimentSet4DNESC5PKTQ9
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Imaging of 1397 cells of Sox2, egfp and mcherry transcripts (RNA-FISH), followed by chromatin tracing of a 210-kb genomic region containing Sox2 and super-enhancer (SE) loci in mouse F123 ESCs with an engineered replacement of 4 CTCF binding sites between Sox2 and SE on the CAST allele of the CAST X 129 hybrid background.

   October 14th, 2021 at 3:33pm
Source Publication
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.
Huang H, Zhu Q, et al., Nature genetics 2021

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 
RMCE
Treatment Type 
None
Assay Details 
Target: 42 consecutive 5-kb loci on chr3 (mouse), Chromosomes, Sox2 mouse transcript, GFP transcript, mCherry transcript
Channel
Imaging Rounds
Path
 
ch04
0
Chromosomes targeted by DAPI
ch03
0-14
505/515nm fiducial beads
ch02
1-14
14 5-kb loci on chr3 (mouse) targeted by oligo probe library, readout probes (with Cy3-labeled imaging oligos).
ch01
1-14
14 5-kb loci on chr3 (mouse) targeted by oligo probe library, readout probes (with Cy5-labeled imaging oligos).
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2 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEXZRASVLC
Bio Rep 1, Tec Rep 1
multiplexed FISH on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE
File
4DNFI9KE6AII
FOF-CT - DNA-spot/trace core (csv)
9.67 MB
File
4DNFI2ZSFLHH
FOF-CT - trace data (csv)
74.59 kB