ExperimentSetReplicate

ExperimentSet4DNESQU9R2NY
released
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Genome-wide chromatin imaging by DNA-MERFISH of 2000 loci in mouse visual cortex of Mecp2 heteozygous knock-out mice, together with RNA-MERFISH of 240 gene transcripts

   July 22nd, 2024 at 9:03pm
Source Publication
Cell type-specific 3D-genome organization and transcription regulation in the brain.
Liu S, Wang CY, et al., Science advances 2025

Note on FOF-CT file format  

FOF-CT Core files replaced  

The original FOF-CT Core files (4DNFICBGS81M, 4DNFI1GVML2C) have been replaced with the current version to correct the 'XYZ_unit' header from 'nm' to 'micron'.

Microscope configuration  

The experiments associated with this study are derived from either d8f51a9c-1e1a-4a6c-9432-ddf7de64e836 or f0172a96-2bf5-4e6a-938d-f205c6e728c9 microscopes

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
tissue
Sample 
visual cortex
Experiment Type(s) 
multiplexed FISH
Modification Type 
None
Treatment Type 
None
Assay Details 
Target: 2000 loci (mouse), Chromosomes, MOp RNA-MERFISH (mouse), Mecp2 mouse protein
Channel
Imaging Rounds
Path
 
ch02
12-87
2000 loci (mouse) targeted by oligo probe library, readout oligo library (with Cy3-labeled imaging oligos)
ch03
12-87
2000 loci (mouse) targeted by oligo probe library, readout oligo library (with Alexa Fluor 647-labeled imaging oligos)
ch04
12-87
2000 loci (mouse) targeted by oligo probe library, readout oligo library (with Alexa Fluor 750-labeled imaging oligos)
ch01
0
540/560nm fiducial beads
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6 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEXO6XHKYI
Bio Rep 1, Tec Rep 1
multiplexed FISH on visual cortex
File
4DNFIJPO3M49
FOF-CT - DNA-spot/trace core (csv)
1.66 GB
File
4DNFI58781OE
FOF-CT - spot demultiplexing (csv)
8.75 GB
File
4DNFIDXFZ3X7
FOF-CT - cell data (csv)
13.67 MB
Experiment
4DNEXT4R491E
Bio Rep 2, Tec Rep 1
multiplexed FISH on visual cortex
File
4DNFIQRRSY2B
FOF-CT - DNA-spot/trace core (csv)
1.64 GB
File
4DNFIV29N6KZ
FOF-CT - spot demultiplexing (csv)
7.9 GB
File
4DNFIVB17XFA
FOF-CT - cell data (csv)
11.02 MB