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Expression data from rice varieties Azucena and Bala grown in 0 and 1ppm arsenate
Gareth,,Norton, University of Aberdeen, Aberdeen, United Kingdom (g.norton@abdn.ac.uk)
Experiment design (12 hybridizations)
cultivar
•Bala •Azucena
compound
•0ppm Arsenate (Control) •1ppm Arsenate

This experiment has been imported by PLEXdb from NCBI GEO (GSE4471)

Series_summary:
We advance a three gene model of arsenate toleran...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Expression data from rice varieties Azucena and Bala grown in 0 and 1ppm arsenate
Accession No: OS11
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
cultivar
•Bala   •Azucena
compound
•0ppm Arsenate (Control)   •1ppm Arsenate
Quality Control: biological replicates
Treatment summary:
 cultivar  compound  # replicates
 Bala  0ppm Arsenate (Control)  3
 Bala  1ppm Arsenate  3
 Azucena  0ppm Arsenate (Control)  3
 Azucena  1ppm Arsenate  3
Total hybridizations: 12
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE4471)

Series_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

Series_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.
Publication: none
Created: 2009-05-01 13:59:06
Last Update: 2009-05-01 14:15:45
GEO Accession GSE4471
Submitter: PLEXdb Curator
Name: Gareth,,Norton
Institution: University of Aberdeen, Aberdeen, United Kingdom
Head of Laboratory: --
email(s):
Homepage:

 
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