Transcriptomics

Dataset Information

6

Transcription profiling by array of Arabidopsis root tips after exposure to hypoxia


ABSTRACT: Plant organs are comprised of distinct cell types with unique assemblages of mRNAs. This is a collection of CEL files of mRNA profiles of the total steady-state mRNAs and polysomal mRNAs of distinct cell types of the root tip of 7-d-old Arabidopsis thaliana seedlings. The cell type specific mRNA populations are those present in ribosome-mRNA complexes. This sub-population of mRNAs was obtained by first establishing a collection of Arabidopsis lines that express a FLAG-epitope tagged ribosomal protein L18 (RPL18) directed by promoters expressed in specific cell types and regions. Four different promoter:FLAG-RPL18 lines were used. The targeted cell types and promoters included root endodermis (pSCR) and root stelar xylem and pericycle (pWOL, pSHR). A CaMV 35S promoter:FLAG-RPL18 line was used to obtain the polysomal mRNA of multiple cell types. The immunopurification of ribosome-mRNA complexes of specific cell types was accomplished by the method described in Zanetti et al. (Plant Physiology, 138, 624-635; 2005). Hybridization of the immunopurified mRNAs to the Affymetrix ATH1 DNA microarray platform and subsequent data analysis permitted the identification of transcripts that are enriched or depleted in specific cell types of root tips. The dataset includes samples from cell types from seedlings grown under control conditions and cell types of seedlings exposed to low oxygen stress (hypoxia) for 2 h. Experiment Overall Design: 20 samples, 2 conditions (2 h hypoxia stress, 2 h non-stress), 2 RNA pools (Total mRNA and polysomal mRNA), 4 promoter lines, 2 replicates

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Angelika Mustroph  

PROVIDER: E-GEOD-14493 | ArrayExpress | 2009-10-20

SECONDARY ACCESSION(S): GSE14493PRJNA114485

REPOSITORIES: GEO, ArrayExpress

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Publications

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis.

Mustroph Angelika A   Zanetti M Eugenia ME   Jang Charles J H CJ   Holtan Hans E HE   Repetti Peter P PP   Galbraith David W DW   Girke Thomas T   Bailey-Serres Julia J  

Proceedings of the National Academy of Sciences of the United States of America 20091020 44


Multicellular organs are composed of distinct cell types with unique assemblages of translated mRNAs. Here, ribosome-associated mRNAs were immunopurified from specific cell populations of intact seedlings using Arabidopsis thaliana lines expressing a FLAG-epitope tagged ribosomal protein L18 (FLAG-RPL18) via developmentally regulated promoters. The profiling of mRNAs in ribosome complexes, referred to as the translatome, identified differentially expressed mRNAs in 21 cell populations defined by  ...[more]

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