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Series GSE4471 Query DataSets for GSE4471
Status Public on Mar 16, 2006
Title Expression data from rice varieties Azucena and Bala grown in 0 and 1ppm arsenate
Organism Oryza sativa
Experiment type Expression profiling by array
Summary We advance a three gene model of arsenate tolerance in rice based on testing root growth of 108 recombinant inbred lines (RILs) of the Bala x Azucena population. Marker genotype at 3 loci determined arsenate tolerance in 99% of RILs tested. Interestingly, plants must inherit 2, but any two alleles from the tolerant parent (Bala) to have the tolerant phenotype. Challenging the Affymetrix GeneChip Rice Genome array with Azucena and Bala RNA isolated from control and arsenate treated plants revealed 592 genes 2 fold-upregulated by arsenate and 696 downregulated. The array data was also used to identify which genes are expressed within the three target loci.
We used microarrays to detail the gene expression at three locations in the rice genome termed AsTol6.1, AsTol6.2 and AsTol10 in response to 1ppm arsenate. The data was also used to study the global gene expression of the two varieties of rice, Azucena and Bala, in the presence of 1ppm arsenate.
Keywords: Hydroponics, 0 and 1ppm sodium arsenate, Rice varieties Azucena and Bala
Overall design Rice varieties Bala and Azucena were grown for 7 days in hydroponics either with or without 1ppm (13.3 uM) arsenate. RNA was harvested from four plants all growing in the same pot for each replicate after measuring the roots lengths to confirm the predicted effect of 1ppm arsenate. The four conditions for each replication were harvested at the same time. Different replicates were grown at different times in independent experiments. A total RNA extraction was performed using the TRIzol method followed by RNA clean up and DNase treatment using the RNeasy clean up method. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug of total RNA followed by hybridization on Affymetrix microarrays.
Contributor(s) Norton G, Nigar M, Williams P, Dasgupta T, Meharg A, Price AH
Citation(s) 18453530
Submission date Mar 15, 2006
Last update date Dec 27, 2017
Contact name Gareth Norton
Organization name University of Aberdeen
Department Plant and Soil Science
Lab Rice genetics
Street address St Machar drive
City Aberdeen
ZIP/Postal code AB24 3UU
Country United Kingdom
Platforms (1)
GPL2025 [Rice] Affymetrix Rice Genome Array
Samples (12)
GSM100439 Rice Azucena 0ppm Arsenate (Control) Rep1
GSM100440 Rice Azucena 0ppm Arsenate (Control) Rep2
GSM100441 Rice Azucena 1ppm Arsenate Rep1
BioProject PRJNA94543

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GSE4471_RAW.tar 54.6 Mb (http)(custom) TAR (of CEL)

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