title: Selective single cell isolation for genomics using microraft arrays.
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.
authors.affiliation: Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Welch
authors.affiliation: iBGS-Integrative Program for Biological & Genome Sciences,3356 Genome Sciences Bldg, CB #7100 Chapel Hill, NC 27599-7100, USA Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors.forename: Lindsay A
authors.initials: LA
authors.lastname: Williams
authors.affiliation: Joint Biomedical Engineering Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: DiSalvo
authors.affiliation: Department of Biology, Campus Box 3280, Coker Hall, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors.forename: Alicia T
authors.initials: AT
authors.lastname: Brandt
authors.affiliation: iBGS-Integrative Program for Biological & Genome Sciences,3356 Genome Sciences Bldg, CB #7100 Chapel Hill, NC 27599-7100, USA.
authors.forename: Raoud
authors.initials: R
authors.lastname: Marayati
authors.affiliation: Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Sims
authors.affiliation: iBGS-Integrative Program for Biological & Genome Sciences,3356 Genome Sciences Bldg, CB #7100 Chapel Hill, NC 27599-7100, USA Joint Biomedical Engineering Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Allbritton
authors.affiliation: Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors.forename: Jan F
authors.initials: JF
authors.lastname: Prins
authors.affiliation: iBGS-Integrative Program for Biological & Genome Sciences,3356 Genome Sciences Bldg, CB #7100 Chapel Hill, NC 27599-7100, USA Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA jen_jen_yeh@med.unc.edu.
authors.forename: Jen Jen
authors.initials: JJ
authors.lastname: Yeh
authors.affiliation: Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Biology, Campus Box 3280, Coker Hall, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA cdjones@email.unc.edu.
authors.forename: Corbin D
authors.initials: CD
authors.lastname: Jones
mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D049109:Cell Proliferation / Q000187:drug effects; D002469:Cell Separation / Q000379:methods*; D002478:Cells, Cultured; D003841:Deoxycytidine / Q000031:analogs & derivatives / Q000494:pharmacology; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D046228:Microarray Analysis; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D014410:Tumor Stem Cell Assay; D000093542:Gemcitabine
chemical_list: D003841:Deoxycytidine; D000093542:Gemcitabine