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Complete sequence-based pathway analysis by differential on-chip DNA and RNA extraction from a single cell.

ABSTRACT: We demonstrate on-chip, differential DNA and RNA extraction from a single cell using a microfluidic chip and a two-stage lysis protocol. This method enables direct use of the whole extract, without additional washing steps, reducing sample loss. Using this method, the tumor driving pathway in individual cells from a colorectal cancer cell line was determined by applying a Bayesian computational pathway model to sequences obtained from the RNA fraction of a single cell and, the mutations driving the pathway were determined by analyzing sequences obtained from the DNA fraction of the same single cell. This combined functional and mutational pathway assessment of a single cell could be of significant value for dissecting cellular heterogeneity in tumors and analyzing single circulating tumor cells.

SUBMITTER: van Strijp D

PROVIDER: S-EPMC5591254 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Complete sequence-based pathway analysis by differential on-chip DNA and RNA extraction from a single cell.

van Strijp D D Vulders R C M RCM Larsen N A NA Schira J J Baerlocher L L van Driel M A MA Pødenphant M M Hansen T S TS Kristensen A A Mir K U KU Olesen T T Verhaegh W F J WFJ Marie R R van der Zaag P J PJ

Scientific reports 20170908 1

We demonstrate on-chip, differential DNA and RNA extraction from a single cell using a microfluidic chip and a two-stage lysis protocol. This method enables direct use of the whole extract, without additional washing steps, reducing sample loss. Using this method, the tumor driving pathway in individual cells from a colorectal cancer cell line was determined by applying a Bayesian computational pathway model to sequences obtained from the RNA fraction of a single cell and, the mutations driving ...[more]

PMID: 28887473

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