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Gene Regulation and Systems Biology

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A Next-Generation Sequencing Approach to Study the Transcriptomic Changes During the Differentiation of Physarum at the Single-Cell Level

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Publication Date: 01 Oct 2012

Type: Original Research

Journal: Gene Regulation and Systems Biology

Citation: Gene Regulation and Systems Biology 2012:6 127-137

doi: 10.4137/GRSB.S10224

Abstract

Physarum polycephalum is a unicellular eukaryote belonging to the amoebozoa group of organisms. The complex life cycle involves various cell types that differ in morphology, function, and biochemical composition. Sporulation, one step in the life cycle, is a stimulus-controlled differentiation response of macroscopic plasmodial cells that develop into fruiting bodies. Well-established Mendelian genetics and the occurrence of macroscopic cells with a naturally synchronous population of nuclei as source of homogeneous cell material for biochemical analyses make Physarum an attractive model organism for studying the regulatory control of cell differentiation. Here, we develop an approach using RNA-sequencing (RNA-seq), without needing to rely on a genome sequence as a reference, for studying the transcriptomic changes during stimulus-triggered commitment to sporulation in individual plasmodial cells. The approach is validated through the obtained expression patterns and annotations, and particularly the results from up- and downregulated genes, which correlate well with previous studies.


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The reviewing and editorial management of our paper was timely, thorough, and systematic.  In particular the reviewers' comments resulted in a paper significantly more robust than the first version.
Dr Clark D Jeffries (University of North Carolina at Chapel Hill, Chapel Hill, NC, USA)
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