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Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes under Salinity Stress during the Vegetative Growth Stage
HARKAMAL WALIA, Department of Botany & Plant Sciecnes ,University of California (waliah02@student.ucr.edu)
Experiment design (11 hybridizations)
genetic line
•FL478 •IR29
stress condition
•control •salt stress

Experiment: "This study provides a genome-wide transcriptional analysis of two well-characterized, genetically related rice genotypes differing ...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes under Salinity Stress during the Vegetative Growth Stage
Accession No: OS2
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
genetic line
•FL478   •IR29
stress condition
•control   •salt stress
Quality Control: biological replicates
Treatment summary:
 genetic line  stress condition  # replicates
 FL478  control  3
 FL478  salt stress  3
 IR29  control  2
 IR29  salt stress  3
Total hybridizations: 11
Description: Experiment:

"This study provides a genome-wide transcriptional analysis of two well-characterized, genetically related rice genotypes differing in salinity tolerance during a gradually imposed salinity stress under greenhouse conditions." This involved, exploration of "the transcriptome of the salt-tolerant(FL478) and salt-sensitive(IR29) genotypes under control and salinity stressed conditions during vegetative growth."

Experiment structure(design):
This experiment has 2 Factors[genetic lines, stress condition].
Factor, genetic line has 2 levels: FL478(salt tolerant) and IR29(salt sensitive standard line).
Factor, stress condition has 2 levels: control and salt-stress.
Each of the 4 treatment factors has 3 replications[except IR29-control which has 2 replications].

Recombinant inbred line FL478(also known as IR66946-3R-178-1-1) is an F2 derived F8 from the cross between Pokkali(salt tolerant indian landrace) and IR29(a salt sensitive standard line).(More details in the publication).

"Genotypes FL478 and IR29 were cultured in sand tanks for 22 d after germination. A gradual salinity treatment was applied at the vegetative stage" for the appropriate treatment group. "Plants were harvested 30 d after germination for expression analysis. Due to gradual imposition and a moderate level of salinity stress induced in the experiment, no visual differences were observed between control and stressed plants for tolerant and sensitive genotypes."

"Plant Culture and Salinity Treatment:
....Salinity treatment was applied by adding NaCl and CaCl2 (5:1 molar concentration) in two steps over a period of 3 d to one reservoir. Electrical conductivities (ECw) of nutrient solutions were monitored using an EC meter daily (Hanna Instruments). The salinity in the treatment reservoir was allowed to stabilize for 5 d to a final electrical conductivity of 7.4 dS m−1. The nonsaline control reservoir with Yoshida solution only had an ECw of 1.1 dS m−1.<9d>

"Total RNA from Crown and growing point tissue was used for expression analysis in control and salt stressed samples." "Approximately 12 plants were dissected to obtain the crown and growing point tissue" and "8 µg of total RNA was processed to produce biotinylated cRNA targets."

"Targets from biological replicates of both genotypes were generated and the expression profiles were determined using Affymetrix Rice Genome arrays."

Sample dates: the submission date at NCBI-GEO has been used in these fields.

Source:
This experiment has been initially submitted to "NCBI GEO (GSE3053)", www.ncbi.nih.gov/geo. The various descriptions in PLEXDB reflects information collected from "NCBI GEO (GSE3053)" and the publication, Walia H. et al. 2005. Plant Physiology 139:822-835.
Publication: none
Created: 2007-08-28 11:23:56
Last Update: 2007-12-21 13:55:39
GEO Accession GSE3053
Submitter: PLEXdb Curator
Name: HARKAMAL WALIA
Institution: Department of Botany & Plant Sciecnes ,University of California
Head of Laboratory: Timothy Close
email(s):
Homepage:

 
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