Rice Array Database

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Experiment ID	GSE4471
Experiment Title	Expression data from rice varieties Azucena and Bala grown in 0 and 1ppm arsenate
Number of Samples	12
Organism(s)	Oryza sativa
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)

Submission date	15-Mar-06
Contact name	Gareth Norton
E-mail(s)	g.norton@abdn.ac.uk
Phone
Fax
URL
Organization name	University of Aberdeen
Department	Plant and Soil Science
Lab	Rice genetics
Street address	St Machar drive
City	Aberdeen
State/province
ZIP/Postal code	AB24 3UU
Country	United Kingdom

	ID	Platform	Sample Name
1.	GSM100439	Affymetrix	Rice Azucena 0ppm Arsenate (Control) Rep1
2.	GSM100440	Affymetrix	Rice Azucena 0ppm Arsenate (Control) Rep2
3.	GSM100441	Affymetrix	Rice Azucena 1ppm Arsenate Rep1
4.	GSM100442	Affymetrix	Rice Azucena 1ppm Arsenate Rep2
5.	GSM100443	Affymetrix	Rice Bala 0ppm Arsenate (Control) Rep1
6.	GSM100444	Affymetrix	Rice Bala 0ppm Arsenate (Control) Rep2
7.	GSM100445	Affymetrix	Rice Bala 1ppm Arsenate Rep1
8.	GSM100446	Affymetrix	Rice Bala 1ppm Arsenate Rep2
9.	GSM149409	Affymetrix	Rice Azucena 0ppm Arsenate (Control) Rep3
10.	GSM149410	Affymetrix	Rice Azucena 1ppm Arsenate Rep3
11.	GSM149411	Affymetrix	Rice Bala 0ppm Arsenate (Control) Rep3
12.	GSM149412	Affymetrix	Rice Bala 1ppm Arsenate Rep3