Open AccessHigh throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq
Author(s) -
Leqian Liu,
Chiraj K. Dalal,
Benjamin M. Heineike,
Adam R. Abate
Publication year - 2019
Publication title -
lab on a chip
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.064
H-Index - 210
eISSN - 1473-0197
pISSN - 1473-0189
DOI - 10.1039/c9lc00084d
Subject(s) - profiling (computer programming) , gene expression profiling , drop (telecommunication) , yeast , gene expression , gene , throughput , biology , computational biology , microbiology and biotechnology , chemistry , genetics , computer science , operating system , telecommunications , wireless
Yeast can be engineered into "living foundries" for non-natural chemical production by reprogramming them via a "design-build-test" cycle. While methods for "design" and "build" are relatively scalable and efficient, "test" remains a bottleneck, limiting the effectiveness of the procedure. Here we describe isogenic colony sequencing (ICO-seq), a massively-parallel strategy to assess the gene expression, and thus engineered pathway efficacy, of large numbers of genetically distinct yeast colonies. We use the approach to characterize opaque-white switching in 658 C. albicans colonies. By profiling the transcriptomes of 1642 engineered S. cerevisiae strains, we assess gene expression heterogeneity in a protein mutagenesis library. Our approach will accelerate synthetic biology by allowing facile and cost-effective transcriptional profiling of large numbers of genetically distinct yeast strains.