This site is devoted to helping people get started with single molecule RNA FISH.  It is an in situ hybridization method that uses probes consisting of multiple oligonucleotides that provide enough sensitivity to enable us to detect individual molecules of RNA inside of single cells while also retaining specificity that allows us to distinguish particular RNA species with a very low false positive rate.  Using this method, you can visualize, localize, and quantify your RNA of interest in cells and tissues.

One of the main goals of the site is to provide answers to some of the common questions that we get when people try out this method.  For those, please see the FAQ.  Another goal is give people some idea what to expect from their experiments.  For some examples, please visit some of our single molecule RNA FISH photo albums.  Also, if you want some references to papers using this method, please check out the papers page.

This site is maintained by the Raj Lab for Systems Biology at University of Pennsylvania and describes a lot of the wisdom we have accumulated over the years in doing RNA FISH.  We have licensed our technology (originally developed in the lab of Sanjay Tyagi and based on the work of Rob Singer) to Biosearch Technologies under the commercial name Stellaris.  We think they do a great job of making the probes, and also take a lot of the headache out of probe synthesis and purification, so we strongly recommend getting started with them.  They have a probe designer online that uses the same algorithms we use internally, and we really recommend using that for designing your probes.


Here's our spot counting software.  Enjoy!