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Series GSE5613 Query DataSets for GSE5613
Status Public on Jan 08, 2007
Title Newbury: Molecular bases of zinc tolerance and accumulation by Arabidopsis halleri
Platform organism Arabidopsis thaliana
Sample organism Arabidopsis halleri
Experiment type Expression profiling by array
Summary This application is from a NERC-funded consortium (Mark MacNair, Nick Smirnoff, Exeter) and (Brian Ford-Lloyd, John Newbury, Birmingham).
Metal tolerance is one of the classic examples of micro-evolution. Despite extensive research the physiological bases of the adaptation in plants are largely unknown. Arabidopsis halleri is a zinc tolerant, zinc accumulating species whereas Arabidopsis petraea is non-accumulating and non-tolerant. The objective of our programme is to identify
a) those key genes that act to determine Zn tolerance and accumulation in Arabidopsis (and which account for the difference in performance of A. halleri and A. petraea grown in the presence of elevated Zn) and
b) those _downstream_ genes that are expressed as part of the tolerance or accumulation response.
Phase 1: Total of 24 chips: Material ready by May 2003 The results will a) tell us how effectively material derived from other Arabidopsis species hybridises to the chips, and b) identify genes that are differentially expressed in the two species in the presence and absence of Zn stress (thus providing initial lists of genes that may be responsible for Zn tolerance or accumulation- but see phase 2)· A. halleri exposed to low and high Zn; root and leaf mRNAs extracted: 3 replicates of each: = 12 slides· A. petraea exposed to low and high Zn; root and leaf mRNAs extracted: 3 replicates of each: = 12 slides
Phase 2: Total of 48 chips: Material ready by September 2003
The results will tell us which genes, identified as having appropriate expression patterns, co-segregate with the Zn tolerance or accumulation phenotype and will provide firmer candidate genes for intensive study. Bulks will be produced from F3 progeny (from the halleri x petraea cross) following phentoypic analyses for Zn tolerance and accumulation.· A bulk of F3 progeny all exhibiting high Zn tolerance: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides· A bulk of F3 progeny all exhibiting low Zn tolerance: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides· A bulk of F3 progeny all exhibiting high Zn accumulation: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides· A bulk of F3 progeny all exhibiting low Zn accumulation: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides

Experimenter name = H. John Newbury
Experimenter phone = 0121 414 5581
Experimenter fax = 0121 414 5925
Experimenter department = Newbury lab
Experimenter institute = University of Birmingham
Experimenter address = School of Biosciences
Experimenter address = University of Birmingham
Experimenter address = Edgbaston
Experimenter address = Birmingham
Experimenter zip/postal_code = B15 2TT
Experimenter country = UK
Keywords: stimulus_or_stress_design; organism_part_comparison_design; strain_or_line_design
 
Overall design 24 samples were used in this experiment
 
Contributor(s) Newbury HJ, Townsend H, Emmerson Z, Schildknecht B
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Aug 25, 2006
Last update date Aug 28, 2018
Contact name Nottingham Arabidopsis Stock Centre (NASC)
E-mail(s) affy@arabidopsis.info
Phone +44 (0)115 951 3237
Fax +44 (0)115 951 3297
URL http://arabidopsis.info/
Organization name Nottingham Arabidopsis Stock Centre (NASC)
Department School of Biosciences, University of Nottingham
Street address Sutton Bonington Campus
City Loughborough
ZIP/Postal code LE12 5RD
Country United Kingdom
 
Platforms (1)
GPL198 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Samples (24)
GSM131079 Newbury_2-1_non-acc-bulk-control-root(NRO)_Rep1_ATH1
GSM131080 Newbury_2-2_non-acc-bulk-control-root(NRO)_Rep2_ATH1
GSM131081 Newbury_2-3_non-acc-bulk-control-root(NRO)_Rep3_ATH1
Relations
BioProject PRJNA96905

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE5613_RAW.tar 51.8 Mb (http)(custom) TAR (of CEL)

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