Hi all, I saw an interesting talk from Mark Krasnow yesterday that made me reconsider some of my planned gene expression experiments and wanted to see what the wise members of the Wormbase community thought. They are trying to understand how lung branching patterns develop by applying many of the principles and approaches from his work in Drosophila; his group is known for beautiful work demonstrating how the Drosophila trachea is patterned. One aspect that stood out was that (obviously) you can’t do saturating genetic screens in mice, the way that one would tackle a patterning problem in more awesome genetic model organisms ;). Instead, he performed single-cell RNA-seq on a range of lung cell-types and through unsupervised clustering was able to construct the gene expression program as cells progressed from precursor cells to the final, differentiated cell-types. In his talk, he argued against whole-tissue or whole-animal gene expression studies from populations, as one can lose interesting information (ie. the variation, which can be informative). Although there were many other interesting aspects to the talk, this particular one resonated for me.
So that brings me to my question: do many have experience with tissue- or cell-specific RNA-seq BUT for single worms? I’m re-thinking some planned experiments and thought it best to consult the community! I know that laser-capture micro-dissection is one possibility. Another approach could be to label and purify the cells or nuclei of interest (ie. with the Steiner/Henikoff biotin acceptor tagging of nuclear pore proteins). I was wondering if any had experience with the strengths/pitfalls of these methods, or alternate ways to do single worm, single cell/tissue RNA-seq?