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High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq

Abstract

Yeasts can be engineered into “living foundries” for non-natural chemical production by reprogramming their genome using a synthetic biology “design-build-test” cycle. While methods for “design” and “build” are scalable and efficient, “test” remains a labor-intensive bottleneck, limiting the effectiveness of the genetic reprogramming results. 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 transcriptomes of 1642 engineered S. cerevisiae strains, we use it to 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.

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Supplementary files

Publication details

The article was received on 24 Jan 2019, accepted on 14 Apr 2019 and first published on 15 Apr 2019


Article type: Paper
DOI: 10.1039/C9LC00084D
Citation: Lab Chip, 2019, Accepted Manuscript

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    High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq

    L. Liu, C. Dalal, B. Heineike and A. R. Abate, Lab Chip, 2019, Accepted Manuscript , DOI: 10.1039/C9LC00084D

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