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Series GSE9278 Query DataSets for GSE9278
Status Public on Oct 01, 2008
Title Transcript profiling of the pea shoot apical meristem highlights processes underlying its function and maintenance
Organism Pisum sativum
Experiment type Expression profiling by array
Summary Plant growth is the result of cell proliferation in the meristems, which requires a dynamic balance between the formation of new tissue and the maintenance of a set of undifferentiated stem cells. There is much that remains unknown about this vital developmental process. In this study, we have reported the generation of 2735 ESTs from three cDNA libraries derived from dissected garden pea (Pisum sativum cv Torsdag) shoot apical meristems. Clustering analysis of the resulting sequences gave rise to 1686 non-redundant ESTs. The unique sequences generated together with 500 other pea transcripts randomly selected from the GenBank pea protein database have been utilized to construct a 2K oligonucleotide array. Using this pea array, we have obtained the transcript profiles of pea shoot apical meristems in comparison to non-apical-meristem tissues. A total of 181 or 174 transcripts were identified to be significantly up- or down-regulated in the pea shoot apical meristem, respectively. As expected, close to 61% of the transcripts down-regulated in the shoot apical mersitem are those retrieved from the public database, whereas sequences from the same source only made up 12% of the genes that were expressed at higher levels in SAMs. This revelation highlights the under-representation of transcripts from the meristmatic tissues in the current public protein database. Manual inspection of the list of up-regulated transcripts reveals the presence of sequences predicted to encode products associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and miRNA regulation. Similar genes have been implicated in the regulation of plant stem cell activity. Taken together, our EST collection as well as the microarray data provides useful starting points for more in depth analysis of the meristem function and maintenance.
Keywords: shoot apical meristem transcript profiling
 
Overall design Total RNA was extracted from dissected SAM (approximately 80 SAMs per extraction) or other plant parts (primary stem, primary roots and mature leaves) using Qiagen RNeasy Mini Kit. Four independent tissue collections and RNA extractions (designated A, B, C and D) were performed for each of the microarray hybridization experiment.The Cy5- or Cy3-labelled cDNA was then hybridized to different sector of the chip according to a balanced block design dual label experiment scheme (Cochran & Cox, 1992):
Sector 1: Cy3-SAM A vs Cy5-NM A
Sector 2: Cy5-SAM B vs Cy3-NM B
Sector 3: Cy3-SAM C vs Cy5-NM C
Sector 4: Cy5-SAM D vs Cy3-NM D
 
Contributor(s) Wong CE, Ottenhof H, Bhalla PL, Singh MB
Citation(s) 18590528
Submission date Oct 09, 2007
Last update date Mar 17, 2012
Contact name Chui E WONG
E-mail(s) acewong@unimelb.edu.au
Organization name University of Melbourne
Department Land and Food
Lab Plant Molecular Biology and Biotechnology Group
Street address University of Melbourne
City Parkville
State/province Victoria
ZIP/Postal code 3010
Country Australia
 
Platforms (1)
GPL5976 UniMelbPea4x2k_ver.1
Samples (4)
GSM235501 DissectedShootApicalMeristem_10-day-oldPea
GSM237071 Pea_Shoot apical meristem 2
GSM237072 Pea_Shoot apical meristem 3
Relations
BioProject PRJNA102909

Download family Format
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9278_RAW.tar 120.0 Kb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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