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Plant Stem Cells pp 113–118Cite as

Mapping a Transcriptome-Guided Arabidopsis SAM Interactome

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2094))

Abstract

The advent of multi-OMICS approaches has a significant impact on the investigation of biological processes occurring in plants. RNA-SEQ, cellular proteomics, and metabolomics have added a considerable ease in studying the dynamics of stem cell niches. New cell sorting approaches coupled with the labeling of stem cell population specific marker genes are highly instrumental in enriching distinct cellular populations for various types of analysis. One more promising field of OMICS is the mapping of cellular interactomes. The plant stem cells research is barely profited from this newly emerging field of OMICS. Generation of stem cell/niche-specific interactome is a time-consuming and labor-intensive task. Here, we describe a method on how to assemble a SAM-based interactome after using the available generic Arabidopsis interactomes. To define the context of SAM in a generic interactome, we used SAM cell population transcriptome datasets. Our step-by-step protocol can easily be adopted for other stem cell niches such as RAM and lateral meristems keeping in view the availability of transcriptome datasets for cellular populations of these niches.

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Acknowledgment

We thank the German Research Foundation (DFG) for funding (TR124/B1) to TD and start-up grant (R18045) and RIF-grant by Zayed University to MN and UAE Space Agency grant (EU1804) to FMH.

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Author notes

  1. Muhammad Naseem and Ozge Osmanoglu contributed equally to this work.

Authors and Affiliations

  1. Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, Abu Dhabi, UAE

    Muhammad Naseem, Jibran Iqbal, Fares M. Howari & Fatima A. AlRemeithi

  2. Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany

    Muhammad Naseem, Ozge Osmanoglu, Martin Kaltdorf & Thomas Dandekar

Authors
  1. Muhammad Naseem
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  2. Ozge Osmanoglu
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  3. Jibran Iqbal
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  4. Fares M. Howari
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  5. Fatima A. AlRemeithi
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  6. Martin Kaltdorf
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  7. Thomas Dandekar
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Corresponding author

Correspondence to Thomas Dandekar .

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Editors and Affiliations

  1. Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, Abu Dhabi, United Arab Emirates

    Muhammad Naseem

  2. Department of Bioinformatics, University of Würzburg, Würzburg, Germany

    Thomas Dandekar

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Naseem, M. et al. (2020). Mapping a Transcriptome-Guided Arabidopsis SAM Interactome. In: Naseem, M., Dandekar, T. (eds) Plant Stem Cells. Methods in Molecular Biology, vol 2094. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0183-9_12

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  • DOI: https://doi.org/10.1007/978-1-0716-0183-9_12

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0182-2

  • Online ISBN: 978-1-0716-0183-9

  • eBook Packages: Springer Protocols

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