This protocol allows image-based transcriptomics as described by Battich, Stoeger et al. 2013 (Nature Methods, Image-based transcriptomics in thousands of single human cells at single-molecule resolution).
When setting up your equipment, run several plates on several different days and biological replicates and monitor multiple wells in the same plates. Only this way you will be able to exclude technical problems. If the absolute spot number is not reproducible you have a problem in your assay (e.g.: cell seeding, FISH protocol or data analysis).
Please download the detailed experimental protocol .
Battich N*, Stoeger T*, Pelkmans L. Image-based transcriptomics in thousands of single human cells at single-molecule resolution. Nat Methods. 2013 Nov;10(11):1127-33. doi: 10.1038/nmeth.2657. Epub 2013 Oct 06. *Contributed equally [Journal]