Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells

Abstract

Provided herein is a method for analyzing cells. In some embodiments the method may comprise base editing a target gene in a population of cells to produce genetically modified cells, reverse transcribing mRNA from single cells in the population of cells to produce cDNA, wherein the cDNA produced by each cell has a cell barcode and a unique molecular identifier (UMI), amplifying and sequencing cDNA transcribed from the target gene, to determine the identity of the edited base, on a cell-by-cell basis, performing gene expression analysis on a cell-by-cell basis using short-read sequencing and comparing the results for each cell, to determine how the edited base alters gene expression.

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