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

Barrantes Bustinza, I. W., Leipzig, J., & Marwan, W. (2012). A Next-Generation Sequencing Approach to Study the Transcriptomic Changes During the Differentiation of Physarum at the Single-Cell Level. Gene Regulation and Systems Biology, 6, 127-137. doi: 10.4137/GRSB.S10224.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0001-235B-2 Version Permalink: http://hdl.handle.net/21.11116/0000-0001-235C-1
Genre: Journal Article

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 Creators:
Barrantes Bustinza, Israel W.1, 2, Author              
Leipzig, Jeremy3, Author
Marwan, Wolfgang2, Author
Affiliations:
1International Max Planck Research School (IMPRS), Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society, ou_1738143              
2Otto-von-Guericke-Universität Magdeburg, External Organizations, ou_1738156              
3Center for Biomedical Informatics, The Children’s Hospital of Philadelphia,, Philadelphia, PA, USA, ou_persistent22              

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 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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Language(s): eng - English
 Dates: 2012
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.4137/GRSB.S10224
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Title: Gene Regulation and Systems Biology
Source Genre: Journal
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Publ. Info: London : Sage
Pages: - Volume / Issue: 6 Sequence Number: - Start / End Page: 127 - 137 Identifier: -