Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana

doi:10.1016/j.gdata.2015.03.015

. 2015 Apr 8:4:96-8.

doi: 10.1016/j.gdata.2015.03.015. eCollection 2015 Jun.

Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana

Daniel Slane¹, Jixiang Kong¹, Markus Schmid², Gerd Jürgens³, Martin Bayer¹

Affiliations

¹ Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
² Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
³ Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany ; Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany.

PMID: 26484189
PMCID: PMC4536148
DOI: 10.1016/j.gdata.2015.03.015

Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana

Daniel Slane et al. Genom Data. 2015.

. 2015 Apr 8:4:96-8.

doi: 10.1016/j.gdata.2015.03.015. eCollection 2015 Jun.

Authors

Daniel Slane¹, Jixiang Kong¹, Markus Schmid², Gerd Jürgens³, Martin Bayer¹

Affiliations

¹ Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
² Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
³ Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany ; Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany.

PMID: 26484189
PMCID: PMC4536148
DOI: 10.1016/j.gdata.2015.03.015

Abstract

In Arabidopsis, various cell type-specific whole-genome expression analyses have been conducted. However, the vast majority of these were performed with cellular RNA from root tissues or other easily accessible cell types [1]. Nuclear RNA was neglected for a long time as not being representative for transcriptomic studies. In recent years, however, there have been reports describing the validity of nuclear RNA for these types of studies [2,3]. Here we describe the generation, quality assessment and analysis of nuclear transcriptomic data from Arabidopsis embryos published by Slane et al. (2014) [4]. Comparison of nuclear with cellular gene expression demonstrated the usefulness of nuclear transcriptomics.

Keywords: Arabidopsis thaliana; Gene expression; Microarray; Nuclear and cellular transcriptome; Pro-embryo and suspensor transcriptome.

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Figures

**Fig. 1**
Quality analysis of extracted RNA. Electropherogram and gel picture for nuclear (A) and cellular (B) RNA.

**Fig. 2**
Correlation analysis of nuclear and cellular expression values. Correlation scatter plot comparing means of log2-transformed expression estimates based on three biological replicates each. Additionally, R value is indicated.

See this image and copyright information in PMC

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References

1. Palovaara J., Saiga S., Weijers D. Transcriptomics approaches in the early Arabidopsis embryo. Trends Plant Sci. 2013;18:514–521. - PubMed
1. Barthelson R.A., Lambert G.M., Vanier C., Lynch R.M., Galbraith D.W. Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells. BMC Genomics. 2007;8:340. - PMC - PubMed
1. Zhang C., Barthelson R.A., Lambert G.M., Galbraith D.W. Global characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiol. 2008;147:30–40. - PMC - PubMed
1. Slane D., Kong J., Berendzen K.W., Kilian J., Henschen A., Kolb M., Schmid M., Harter K., Mayer U., De Smet I., Bayer M., Jürgens G. Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development. 2014;141:4831–4840. - PubMed
1. Khodosevich K., Inta D., Seeburg P.H., Monyer H. Gene expression analysis of in vivo fluorescent cells. PLoS ONE. 2007;2:e1151. - PMC - PubMed

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[1] Palovaara J., Saiga S., Weijers D. Transcriptomics approaches in the early Arabidopsis embryo. Trends Plant Sci. 2013;18:514–521. - PubMed

[2] Palovaara J., Saiga S., Weijers D. Transcriptomics approaches in the early Arabidopsis embryo. Trends Plant Sci. 2013;18:514–521. - PubMed

[3] Barthelson R.A., Lambert G.M., Vanier C., Lynch R.M., Galbraith D.W. Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells. BMC Genomics. 2007;8:340. - PMC - PubMed

[4] Barthelson R.A., Lambert G.M., Vanier C., Lynch R.M., Galbraith D.W. Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells. BMC Genomics. 2007;8:340. - PMC - PubMed

[5] Zhang C., Barthelson R.A., Lambert G.M., Galbraith D.W. Global characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiol. 2008;147:30–40. - PMC - PubMed

[6] Zhang C., Barthelson R.A., Lambert G.M., Galbraith D.W. Global characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiol. 2008;147:30–40. - PMC - PubMed

[7] Slane D., Kong J., Berendzen K.W., Kilian J., Henschen A., Kolb M., Schmid M., Harter K., Mayer U., De Smet I., Bayer M., Jürgens G. Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development. 2014;141:4831–4840. - PubMed

[8] Slane D., Kong J., Berendzen K.W., Kilian J., Henschen A., Kolb M., Schmid M., Harter K., Mayer U., De Smet I., Bayer M., Jürgens G. Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development. 2014;141:4831–4840. - PubMed

[9] Khodosevich K., Inta D., Seeburg P.H., Monyer H. Gene expression analysis of in vivo fluorescent cells. PLoS ONE. 2007;2:e1151. - PMC - PubMed

[10] Khodosevich K., Inta D., Seeburg P.H., Monyer H. Gene expression analysis of in vivo fluorescent cells. PLoS ONE. 2007;2:e1151. - PMC - PubMed

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Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana

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Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana

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