A Color Portrait of the Transcriptome in Thousands of Cells

October 7, 2013 | A new technique is allowing researchers at the University of Zurich to visualize the quantity and location of transcript molecules inside thousands of functioning cells at once. Fluorescent stains have previously been used to measure gene activity in single cells, by illuminating the transcript molecules produced when a specific gene is activated. However, the method has not scaled well, either for many genes in a single cell or for one gene across many cells. Now, Prof. Lucas Pelkmans at Zurich has devised an automated technique for rapidly staining many transcript molecules with distinct fluorescent tags, and analyzing the images obtained through a fluorescence microscope using ETH Zurich’s supercomputer Brutus. With this procedure, Prof. Pelkmans’ lab can simultaneously track a thousand different transcript molecules across ten thousand cells, offering a much more complete picture of gene activity as it is expressed within an organism. The technique is already demonstrating that the spatial organization of different transcript molecules in the cell varies considerably – and that genes with similar functions tend to produce transcript molecules with similar spatial arrangements. Nature Methods