ExperimentSetReplicate

ExperimentSet4DNESL2AY9CM
released
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Integrated spatial genomics in mouse ES cells: 2460 loci across the whole genome at 1-Mb resolution and 1200 loci across 20 regions at 25-kb resolution (DNA seqFISH+), 70 mRNAs or introns (RNA seqFISH), 17 chromatin marks and nuclear bodies (sequential IF)

   May 12th, 2022 at 9:47am
Source Publication
Integrated spatial genomics reveals global architecture of single nuclei.
Takei Y, Yun J, et al., Nature 2021

Note on FOF-CT file format  

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
stem cells
Sample 
ES-E14TG2a.4
Experiment Type(s) 
multiplexed FISH
Modification Type 
None
Treatment Type 
None
Assay Details 
Target: 70 RNAs (mouse), 7 genomic regions, 17 proteins, Chromosomes
Channel
Imaging Rounds
Path
 
ch01
1-80
1267 loci (mouse) targeted by oligo probe library (with Alexa Fluor 647-labeled imaging oligos)
ch02
1-80
1193 loci (mouse) targeted by oligo probe library (with Cy3B-labeled imaging oligos)
ch03
1-80
1200 loci from 20 regions at 25-kb resolution (mouse) targeted by oligo probe library (with Alexa Fluor 488-labeled imaging oligos)
ch01
-
35 RNAs (mouse) targeted by oligo probe library (with Alexa Fluor 647-labeled imaging oligos)
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12 Processed Files

Experiment
File
File Type
File Size
Notes
Experiment
4DNEXM45AILX
Bio Rep 1, Tec Rep 1
multiplexed FISH on ES-E14TG2a.4
File
4DNFIFLJGGNR
FOF-CT - DNA-spot/trace core (csv)
44.91 MB
File
4DNFIHF3JCBY
FOF-CT - DNA-spot/trace core (csv)
20.85 MB
File
4DNFIJ52NVDV
FOF-CT - RNA-spot (csv)
214.33 kB
-
File
4DNFIFINA2U9
FOF-CT - cell data (csv)
57.05 kB
-
File
4DNFIHXXYAD3
FOF-CT - spot quality (csv)
9.66 MB
File
4DNFIRU2BP2B
FOF-CT - spot quality (csv)
23.47 MB
Experiment
4DNEXLZAD21X
Bio Rep 2, Tec Rep 1
multiplexed FISH on ES-E14TG2a.4
File
4DNFIBLDQPP7
FOF-CT - DNA-spot/trace core (csv)
69.32 MB
File
4DNFIQXONUUH
FOF-CT - DNA-spot/trace core (csv)
32.53 MB
File
4DNFIYW8TTK7
FOF-CT - RNA-spot (csv)
286.25 kB
-
File
4DNFIF78A5D4
FOF-CT - cell data (csv)
64.73 kB
-
File
4DNFI2MJB3U7
FOF-CT - spot quality (csv)
15.04 MB
File
4DNFI234A77K
FOF-CT - spot quality (csv)
37.08 MB