Single cell transcriptomics in plant systems

In recent years, the study of mRNA expression has been transformed by next generation sequencing (RNA-Seq), which enables the simultaneous measurement of the steady-state transcription levels of thousands of genes with a dynamic range of many orders of magnitude. It offers additional benefits, such as the ability to distinguish alternatively spliced transcripts, and identify preferential expression of one allele over another. However, RNA-Seq so practiced tends to be imprecise, in large part because the RNA input requirements require that entire tissues are pooled before RNA extraction and sequencing. Consequently, RNA expression levels are usually reported in, for example, entire leaves or root systems, when in fact, the interesting biology may be occurring in a single cell type or in particular individual cells.

Publications

  • J. Sena, G. Galotto, N. Devitt, M. Connick, J. Jacobi, P. Umale, L. Vidali and C. Bell.
    Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis
    Sci Rep (PMID: 30177820), 8(1), 13121, 2018
    Single cell transcriptomics in plant systems 

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