Abstract
Cell type-specific gene expression profiles are useful for understanding genes that are important for the development of different tissues and organs. Here, we describe how to perform fluorescence-activated cell sorting (FACS) on Arabidopsis root protoplasts to isolate specific cell types in the root. We then detail how to extract and process RNA from a very low number of cells (≥40 cells) for RNA sequencing (RNA seq). Finally, we describe how to process RNA seq data using TopHat and how to identify differentially expressed genes using PoissonSeq.
Natalie M. Clark and Adam P. Fisher contributed equally to this work.
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References
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Acknowledgments
N.M.C. and A.P.F. are supported by an NSF GRF (DGE-1252376). This work was funded by an NSF CAREER grant (MCB-1453130) and by the Bilateral BBSRC NSF/BIO (MCB-1517058) to R.S.
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Clark, N.M., Fisher, A.P., Sozzani, R. (2018). Identifying Differentially Expressed Genes Using Fluorescence-Activated Cell Sorting (FACS) and RNA Sequencing from Low Input Samples. In: von Stechow, L., Santos Delgado, A. (eds) Computational Cell Biology. Methods in Molecular Biology, vol 1819. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8618-7_6
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DOI: https://doi.org/10.1007/978-1-4939-8618-7_6
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