Unknown,Transcriptomics,Genomics,Proteomics

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A transcriptional map following the developmental trajectory of the Arabidopsis stomatal lineage


ABSTRACT: Developmental transitions can be described in terms of morphology and individual genes expression patterns, but also in terms of global transcriptional and epigenetic changes. Most of the large-scale studies of such transitions, however, have only been possible in synchronized cell culture systems. Here we generate a cell type specific transcriptome of an adult stem-cell lineage in the Arabidopsis leaf using RNA sequencing and microarrays. RNA profiles of stomatal entry, commitment, and differentiating cells, as well as of mature stomata and the entire aerial epidermis give a comprehensive view of the developmental progression. To obtain pure cell populations corresponding to different stomatal lineage cell types we used Fluorescent Activated Cell Sorting (FACS) in combination with markers of early (SPCHp::SPCH-YFP, SSY), middle (MUTEp::nucGFP, MG), and late (FAMAp::GFP-FAMA, FGF) precursor stages, as well of mature stomata (enhancer trap E1728::GFP, E1728G) and a marker of the entire epidermis (ML1p::YFP-RCI2A, ML1Y). To minimize transcriptional differences due to age, all cell types were sorted from 14-day old aerial rosettes, and the specificity of expression pattern at this common time point confirmed via confocal microscopy. Total RNA was extracted from purified protoplasts (2,000 to 20,000 cells/replicate; 3 replicates/marker line) and transcript abundance measured using ATH1-121501 microarrays.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Dominique Bergmann 

PROVIDER: E-GEOD-58855 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population.

Adrian Jessika J   Chang Jessica J   Ballenger Catherine E CE   Bargmann Bastiaan O R BO   Alassimone Julien J   Davies Kelli A KA   Lau On Sun OS   Matos Juliana L JL   Hachez Charles C   Lanctot Amy A   Vatén Anne A   Birnbaum Kenneth D KD   Bergmann Dominique C DC  

Developmental cell 20150401 1


Developmental transitions can be described in terms of morphology and the roles of individual genes, but also in terms of global transcriptional and epigenetic changes. Temporal dissections of transcriptome changes, however, are rare for intact, developing tissues. We used RNA sequencing and microarray platforms to quantify gene expression from labeled cells isolated by fluorescence-activated cell sorting to generate cell-type-specific transcriptomes during development of an adult stem-cell line  ...[more]

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