Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. 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. Development (Cambridge, England), 141(24):4831–4840, December, 2014. doi abstract bibtex In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.
@article{slane_cell_2014,
title = {Cell type-specific transcriptome analysis in the early {Arabidopsis} thaliana embryo},
volume = {141},
issn = {1477-9129},
doi = {10/f6s68v},
abstract = {In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.},
language = {eng},
number = {24},
journal = {Development (Cambridge, England)},
author = {Slane, Daniel and Kong, Jixiang and Berendzen, Kenneth W. and Kilian, Joachim and Henschen, Agnes and Kolb, Martina and Schmid, Markus and Harter, Klaus and Mayer, Ulrike and De Smet, Ive and Bayer, Martin and Jürgens, Gerd},
month = dec,
year = {2014},
pmid = {25411212},
keywords = {Arabidopsis, Cell Nucleus, Cloning, Molecular, Fluorescence-activated nuclear sorting, Gene Expression Profiling, Genotype, In Situ Hybridization, Microarray Analysis, Microscopy, Fluorescence, Proembryo, RNA, Nuclear, Real-Time Polymerase Chain Reaction, Seeds, Suspensor, Transcriptome analysis},
pages = {4831--4840},
}
Downloads: 0
{"_id":"dkPMRS9WxzThfdtvg","bibbaseid":"slane-kong-berendzen-kilian-henschen-kolb-schmid-harter-etal-celltypespecifictranscriptomeanalysisintheearlyarabidopsisthalianaembryo-2014","author_short":["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."],"bibdata":{"bibtype":"article","type":"article","title":"Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo","volume":"141","issn":"1477-9129","doi":"10/f6s68v","abstract":"In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.","language":"eng","number":"24","journal":"Development (Cambridge, England)","author":[{"propositions":[],"lastnames":["Slane"],"firstnames":["Daniel"],"suffixes":[]},{"propositions":[],"lastnames":["Kong"],"firstnames":["Jixiang"],"suffixes":[]},{"propositions":[],"lastnames":["Berendzen"],"firstnames":["Kenneth","W."],"suffixes":[]},{"propositions":[],"lastnames":["Kilian"],"firstnames":["Joachim"],"suffixes":[]},{"propositions":[],"lastnames":["Henschen"],"firstnames":["Agnes"],"suffixes":[]},{"propositions":[],"lastnames":["Kolb"],"firstnames":["Martina"],"suffixes":[]},{"propositions":[],"lastnames":["Schmid"],"firstnames":["Markus"],"suffixes":[]},{"propositions":[],"lastnames":["Harter"],"firstnames":["Klaus"],"suffixes":[]},{"propositions":[],"lastnames":["Mayer"],"firstnames":["Ulrike"],"suffixes":[]},{"propositions":[],"lastnames":["De","Smet"],"firstnames":["Ive"],"suffixes":[]},{"propositions":[],"lastnames":["Bayer"],"firstnames":["Martin"],"suffixes":[]},{"propositions":[],"lastnames":["Jürgens"],"firstnames":["Gerd"],"suffixes":[]}],"month":"December","year":"2014","pmid":"25411212","keywords":"Arabidopsis, Cell Nucleus, Cloning, Molecular, Fluorescence-activated nuclear sorting, Gene Expression Profiling, Genotype, In Situ Hybridization, Microarray Analysis, Microscopy, Fluorescence, Proembryo, RNA, Nuclear, Real-Time Polymerase Chain Reaction, Seeds, Suspensor, Transcriptome analysis","pages":"4831–4840","bibtex":"@article{slane_cell_2014,\n\ttitle = {Cell type-specific transcriptome analysis in the early {Arabidopsis} thaliana embryo},\n\tvolume = {141},\n\tissn = {1477-9129},\n\tdoi = {10/f6s68v},\n\tabstract = {In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.},\n\tlanguage = {eng},\n\tnumber = {24},\n\tjournal = {Development (Cambridge, England)},\n\tauthor = {Slane, Daniel and Kong, Jixiang and Berendzen, Kenneth W. and Kilian, Joachim and Henschen, Agnes and Kolb, Martina and Schmid, Markus and Harter, Klaus and Mayer, Ulrike and De Smet, Ive and Bayer, Martin and Jürgens, Gerd},\n\tmonth = dec,\n\tyear = {2014},\n\tpmid = {25411212},\n\tkeywords = {Arabidopsis, Cell Nucleus, Cloning, Molecular, Fluorescence-activated nuclear sorting, Gene Expression Profiling, Genotype, In Situ Hybridization, Microarray Analysis, Microscopy, Fluorescence, Proembryo, RNA, Nuclear, Real-Time Polymerase Chain Reaction, Seeds, Suspensor, Transcriptome analysis},\n\tpages = {4831--4840},\n}\n\n","author_short":["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."],"key":"slane_cell_2014","id":"slane_cell_2014","bibbaseid":"slane-kong-berendzen-kilian-henschen-kolb-schmid-harter-etal-celltypespecifictranscriptomeanalysisintheearlyarabidopsisthalianaembryo-2014","role":"author","urls":{},"keyword":["Arabidopsis","Cell Nucleus","Cloning","Molecular","Fluorescence-activated nuclear sorting","Gene Expression Profiling","Genotype","In Situ Hybridization","Microarray Analysis","Microscopy","Fluorescence","Proembryo","RNA","Nuclear","Real-Time Polymerase Chain Reaction","Seeds","Suspensor","Transcriptome analysis"],"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://bibbase.org/zotero/upscpub","dataSources":["9cGcv2t8pRzC92kzs","fvfkWcShg3Mybjoog","Tu3jPdZyJF3j547xT"],"keywords":["arabidopsis","cell nucleus","cloning","molecular","fluorescence-activated nuclear sorting","gene expression profiling","genotype","in situ hybridization","microarray analysis","microscopy","fluorescence","proembryo","rna","nuclear","real-time polymerase chain reaction","seeds","suspensor","transcriptome analysis"],"search_terms":["cell","type","specific","transcriptome","analysis","early","arabidopsis","thaliana","embryo","slane","kong","berendzen","kilian","henschen","kolb","schmid","harter","mayer","de smet","bayer","jürgens"],"title":"Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo","year":2014}