Left: Single molecule RNA detection. Center: Stained membranes and nuclei. Right: Automated detection of transcripts (magenta), transcription foci (white), membranes (green) and nuclei (blue)
The Vastenhouw Lab presents a method for automated transcript detection using single molecule fluorescence in situ hybridization (smFISH) in combination with an automated image analysis pipeline. This strategy will enable researchers to analyze gene expression at single molecule resolution in complex tissues and embryos. So far, protocols that enabled quantitative transcript analyses at cellular and subcellular resolution in tissues and embryos did not exist.
The approach by the Vastenhouw lab now fills this gap, and combining it with an analysis pipeline for automated transcript detection and cell segmentation makes it a very powerful tool. “We demonstrated the versatility of our method by quantifying RNA expression in single cells of developing zebrafish embryos,” says Carine Stapel, first author of the publication that presents the new method. The project was a collaboration of Nadine Vastenhouw’s research group with the Myers Lab and the Scientific Computing Facility at the MPI-CBG.
L. Carine Stapel, Benoit Lombardot, Coleman Broaddus, Dagmar Kainmueller, Florian Jug, Eugene W. Myers, Nadine L. Vastenhouw:
Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos
Development 2015 : doi: 10.1242/dev.128918