Gene expression profiling of single epidermal, basal and trichome cells of Arabidopsis thaliana.

Lieckfeldt, E; Simon-Rosin, U; Kose, F; Zoeller, D; Schliep, M; Fisahn, J

Gene expression profiling of single epidermal, basal and trichome cells of Arabidopsis thaliana.

Lieckfeldt, E Simon-Rosin, U Kose, F Zoeller, D Schliep, M Fisahn, J

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Publication Type:: Journal Article
Citation:: J Plant Physiol, 2008, 165 (14), pp. 1530 - 1544
Issue Date:: 2008-09-29

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Field	Value	Language
dc.contributor.author	Lieckfeldt, E	en_US
dc.contributor.author	Simon-Rosin, U	en_US
dc.contributor.author	Kose, F	en_US
dc.contributor.author	Zoeller, D	en_US
dc.contributor.author	Schliep, M	en_US
dc.contributor.author	Fisahn, J	en_US
dc.date.available	2007-06-10	en_US
dc.date.issued	2008-09-29	en_US
dc.identifier.citation	J Plant Physiol, 2008, 165 (14), pp. 1530 - 1544	en_US
dc.identifier.uri	http://hdl.handle.net/10453/31181
dc.description.abstract	Samples of single epidermal, basal and trichome cells were collected by glass microcapillaries from 7-week-old Arabidopsis thaliana leaves. Transcript amplification of these single-cell samples was performed by RT PCR. For gene expression profiling, we hybridized the amplified transcriptome of each individual cell type to nylon membranes spotted with 16,000 Arabidopsis expressed sequence tags (ESTs). Initial analysis of the array filter data enabled us to functionally categorize transcripts that were present in each individual cell type. In order to confirm the filter array data, we used RT PCR. Results of this RT PCR approach confirmed the presence of 12 selected candidate genes in agreement with array filter hybridization data. Further, transcripts involved in detoxification and sulfur metabolism could be identified in epidermal cell extracts. Together, the results of our study provide the localization of approximately 1000 expressed genes to either pavement, basal or trichome cells. To cluster transcripts with similar expression levels, we developed a novel mathematical algorithm. Based on the mean and standard deviation, ratios of expression levels of a transcript were defined for pairs of the three cell types. This numerical analysis enabled subdivision into 67 categories of genes differentially expressed in epidermal, basal and trichome cells. Transcripts in each category displayed similar ratios of expression levels in the three cell types. Examples of these clusters are presented and discussed in Appendix A.	en_US
dc.language	eng	en_US
dc.relation.ispartof	J Plant Physiol	en_US
dc.relation.isbasedon	10.1016/j.jplph.2007.06.017	en_US
dc.subject.classification	Plant Biology & Botany	en_US
dc.subject.mesh	Arabidopsis	en_US
dc.subject.mesh	Plant Epidermis	en_US
dc.subject.mesh	Plant Leaves	en_US
dc.subject.mesh	Sulfur	en_US
dc.subject.mesh	Oligonucleotide Array Sequence Analysis	en_US
dc.subject.mesh	Gene Expression Profiling	en_US
dc.subject.mesh	Gene Expression Regulation, Plant	en_US
dc.subject.mesh	Metabolic Detoxication, Drug	en_US
dc.subject.mesh	Genes, Plant	en_US
dc.subject.mesh	Inactivation, Metabolic	en_US
dc.title	Gene expression profiling of single epidermal, basal and trichome cells of Arabidopsis thaliana.	en_US
dc.type	Journal Article
utslib.citation.volume	14	en_US
utslib.citation.volume	165	en_US
utslib.location.activity	Germany	en_US
utslib.for	0607 Plant Biology	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
utslib.copyright.status	closed_access
pubs.issue	14	en_US
pubs.publication-status	Published	en_US
pubs.volume	165	en_US

Abstract:

Samples of single epidermal, basal and trichome cells were collected by glass microcapillaries from 7-week-old Arabidopsis thaliana leaves. Transcript amplification of these single-cell samples was performed by RT PCR. For gene expression profiling, we hybridized the amplified transcriptome of each individual cell type to nylon membranes spotted with 16,000 Arabidopsis expressed sequence tags (ESTs). Initial analysis of the array filter data enabled us to functionally categorize transcripts that were present in each individual cell type. In order to confirm the filter array data, we used RT PCR. Results of this RT PCR approach confirmed the presence of 12 selected candidate genes in agreement with array filter hybridization data. Further, transcripts involved in detoxification and sulfur metabolism could be identified in epidermal cell extracts. Together, the results of our study provide the localization of approximately 1000 expressed genes to either pavement, basal or trichome cells. To cluster transcripts with similar expression levels, we developed a novel mathematical algorithm. Based on the mean and standard deviation, ratios of expression levels of a transcript were defined for pairs of the three cell types. This numerical analysis enabled subdivision into 67 categories of genes differentially expressed in epidermal, basal and trichome cells. Transcripts in each category displayed similar ratios of expression levels in the three cell types. Examples of these clusters are presented and discussed in Appendix A.

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http://hdl.handle.net/10453/31181