Selective single cell isolation for genomics using microraft arrays

Joshua D. Welch, Lindsay A. Williams, Matthew DiSalvo, Alicia T. Brandt, Raoud Marayati, Christopher E. Sims, Nancy L. Allbritton, Jan F. Prins, Jen Jen Yeh, Corbin D. Jones

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

Genomic methods are used increasingly to interrogate the individual cells that compose specific tissues. However, current methods for single cell isolation struggle to phenotypically differentiate specific cells in a heterogeneous population and rely primarily on the use of fluorescent markers. Many cellular phenotypes of interest are too complex to be measured by this approach, making it difficult to connect genotype and phenotype at the level of individual cells. Here we demonstrate that microraft arrays, which are arrays containing thousands of individual cell culture sites, can be used to select single cells based on a variety of phenotypes, such as cell surface markers, cell proliferation and drug response. We then show that a common genomic procedure, RNA-seq, can be readily adapted to the single cells isolated from these rafts. We show that data generated using microrafts and our modified RNA-seq protocol compared favorably with the Fluidigm C1. We then used microraft arrays to select pancreatic cancer cells that proliferate in spite of cytotoxic drug treatment. Our single cell RNA-seq data identified several expected and novel gene expression changes associated with early drug resistance.

Original languageEnglish (US)
Pages (from-to)8292-8301
Number of pages10
JournalNucleic acids research
Volume44
Issue number17
DOIs
StatePublished - Sep 30 2016

Bibliographical note

Funding Information:
NCBC [2013-MRG-1110, in part to C.D.J.]; UCRF (in part to C.D.J.); National Science Foundation (NSF) [ABI/EF0850237 to J.F.P.]; National Institutes of Health (NIH) [R43EB019752 to N.L.A.]; NSF Graduate Research Fellowship [DGE-1144081 to J.D.W.]; NIH BD2K Fellowship [T32 CA201159 to J.D.W.]. Funding for open access charge: NCBC [2013-MRG-1110].

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