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Browse RicePLEX Experiment Data

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Transcription profiling of parental lines and bulked salt sensitive and salt tolerant RILs derived from 2 rice varieties
Awadhesh Pandit, NRC on Plant Biotechnology, Rice Genome Lab, New Delhi, India (awadheshpandit@gmail.com,nksingh@nrcpb.org)
Experiment design (16 hybridizations)
genetic line
•MI48 •CSR27 •Bulk tolerant •Bulk sensitive
stress condition
•control •salt stressed

This experiment has been imported by PLEXdb from NCBI GEO (GSE16108) Series_summary: The aim of this study was to minimize the number of candi...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Transcription profiling of parental lines and bulked salt sensitive and salt tolerant RILs derived from 2 rice varieties
Accession No: OS50
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
genetic line
•MI48   •CSR27   •Bulk tolerant   •Bulk sensitive
stress condition
•control   •salt stressed
Quality Control: biological replicates
Treatment summary:
 genetic line  stress condition  # replicates
 MI48  control  2
 MI48  salt stressed  2
 CSR27  control  2
 CSR27  salt stressed  2
 Bulk tolerant  control  2
 Bulk tolerant  salt stressed  2
 Bulk sensitive  control  2
 Bulk sensitive  salt stressed  2
Total hybridizations: 16
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE16108)

Series_summary:
The aim of this study was to minimize the number of candidate genes responsible for salt tolerance between a pair of rice varieties (CSR27 and MI48) with contrasting level of salt tolerance by bulked segregant analysis of their recombinant inbred lines. Microarray analysis of RNA extracted from the tolerant and susceptible parents without and with stress showed 798 and 2407 differentially expressed genes, respectively. The number of differentially expressed genes was drastically reduced to 70 and 30, by pooling the RNAs from ten extreme tolerant and ten extreme susceptible RILs due to normalization of irrelevant differentially expressed genes between the parents.

Series_overall_design:
RNA from CSR27, MI48, tolerant bulk and susceptible bulk grown under control and salt stress conditions were analysed in two different biological replications (A and B) making total sixteen samples
Publication: 'Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.).', Pandit A, Rai V, Bal S, Sinha S, Kumar V, Chauhan M, Gautam RK, Singh R, Sharma PC, Singh AK, Gaikwad K, Sharma TR, Mohapatra T, Singh NK.
Mol Genet Genomics 2010 Aug;284(2):121-36.
pubmed: 20602115
Created: 2011-03-31 12:20:43
Last Update: 2011-03-31 12:43:58
Released: 2011-04-15
GEO Accession GSE16108
Submitter: PLEXdb Curator
Name: Awadhesh Pandit
Institution: NRC on Plant Biotechnology, Rice Genome Lab, New Delhi, India
Head of Laboratory: Nagendra K. Singh
email(s):
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