Transcriptomics,Multiomics

Dataset Information

332

Molecular Dissection of Pea Shoot Apical Meristem


ABSTRACT: Knowledge about an organism’s cell and tissue-specific transcriptional repertoire is essential for understanding the gene regulatory circuits that control key developmental events. The shoot apical meristem (SAM) is responsible for development of all the above ground parts of plants. Our understanding of SAM at the molecular level is far from complete. The present work investigates the global gene expression repertoire of SAMs in the garden pea (Pisum sativum). To this end, 10,346 EST sequences representing 7611 unique genes were generated from pea SAM cDNA libraries. These sequences, together with previously reported ESTs, were used to construct a 12K oligonucleotide array used to identify genes exhibiting differential SAM expression, as compared to the axillary meristem, root apical meristem, and non-meristematic tissues. We identified a number of genes that are predominantly expressed in specific cell layers or domains of the SAM, and thus are likely components of the gene networks involved in stem cell maintenance and initiation of lateral organ primordial cells. In situ hybridization confirmed the spatial localisation of some of these key genes within the SAM. Our data also indicate the diversification of some gene expression patterns and functions in legume crop plants. RNA samples were hybridized to two-colour Combimatrix arrays manufactured with a custom library of 11958 probes. The limma software package for R (Smyth, 2005) was used in subsequent statistical analysis of the data generated. On examination of the data during quality control assessment, it became evident that the Cy3 channel showed little dynamic range and background correction and normalisation could not correct for this. Therefore only the Cy5 channel was used in the subsequent analysis. This resulted in somewhat unbalanced sample sizes with six replicates of SAM and one each of RAM, AM and NM. Nevertheless, linear modelling and empirical Bayes moderated t-statistics (Smyth, 2004) used in the statistical analysis allows variance information to be borrowed across both samples and genes, resulting in reliable statistical inference even for the groups with only one sample.

OTHER RELATED OMICS DATASETS IN: PRJNA110051

ORGANISM(S): Pisum sativum  

SUBMITTER: Gordon Smyth   Prem L Bhalla   Chui E Wong  Chui E WONG  Belinda Phipson  Dacheng Liang  Mohan B Singh 

PROVIDER: E-GEOD-13451 | ArrayExpress | 2010-06-20

SECONDARY ACCESSION(S): GSE13451PRJNA110051

REPOSITORIES: GEO, ArrayExpress

Dataset's files

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E-GEOD-13451.README.txt Txt
E-GEOD-13451.idf.txt Idf
E-GEOD-13451.processed.1.zip Processed
E-GEOD-13451.sdrf.txt Txt
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Publications

Molecular dissection of the pea shoot apical meristem.

Liang Dacheng D   Wong Chui E CE   Singh Mohan B MB   Beveridge Christine A CA   Phipson Belinda B   Smyth Gordon K GK   Bhalla Prem L PL  

Journal of experimental botany 20090825 14


The shoot apical meristem (SAM) is responsible for the development of all the above-ground parts of a plant. Our understanding of the SAM at the molecular level is incomplete. This study investigates the gene expression repertoire of SAMs in the garden pea (Pisum sativum). To this end, 10 346 EST sequences representing 7610 unique genes were generated from SAM cDNA libraries. These sequences, together with previously reported pea ESTs, were used to construct a 12K oligonucleotide array to identi  ...[more]

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