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| Status |
Public on Dec 31, 2021 |
| Title |
Analysis of the transcriptomes of salt tolerant and susceptible cultivars of indica rice by microarray |
| Platform organism |
Oryza sativa |
| Sample organism |
Oryza sativa Indica Group |
| Experiment type |
Expression profiling by array
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| Summary |
Over the years, many traditional rice varietites of India were sourced and studied owing to their ability to withstand abiotic pressures like excessive salinity in the soil and water. These cultivars growing in specific areas of the country represent a rich gene pool from where a deeper understanding of the processes underlying tolerance to abiotic stress can be gained. Indigenous varieties like Nonabokra and Pokkali are known salt tolerant varieties and are being studied in great detail. In the present study, we have analyzed the transcriptomes of the contrasting cultivars; Nonabokra (tolerant), Pokkali (tolerant) and IR29 (susceptible) in order to decipher the differences in their responses to salinity stress by utilizing microarray.
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| Overall design |
Seedlings of Nonabokra, Pokkali and IR29 were grown hydropnically for seven days and then subjected to salinity stress by placing them in 200 mM NaCl solution under light for 3 h and 6 h at 28±1oC. For control samples, seedlings were kept in RGM (root growth medium) for 6 h at 28±1oC. RNA extracted from each sample was hybridized on rice Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. Overall, twenty seven samples were analyzed representing control, 3 h and 6 h of salinity stress for each cultivar (Nonabokra, Pokkali and IR29).
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| Contributor(s) |
Borah P, Kapoor S, Khurana JP |
| Citation missing |
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| Submission date |
Oct 17, 2012 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Jitendra Paul Khurana |
| E-mail(s) |
khuranaj@genomeindia.org
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| Phone |
91 11 24115126
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| Organization name |
University of Delhi South Campus
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| Department |
Department of Plant Molecular Biology
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| Street address |
Benito Juarez Road
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| City |
New Delhi |
| ZIP/Postal code |
110021 |
| Country |
India |
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| Platforms (1) |
| GPL2025 |
[Rice] Affymetrix Rice Genome Array |
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| Samples (27)
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| GSM1020968 |
Control Nonabokra 7-day-old seedling, Biological replicate 1 |
| GSM1020969 |
Control Nonabokra 7-day-old seedling, Biological replicate 2 |
| GSM1020970 |
Control Nonabokra 7-day-old seedling, Biological replicate 3 |
| GSM1020971 |
Control Pokkali 7-day-old seedling, Biological replicate 1 |
| GSM1020972 |
Control Pokkali 7-day-old seedling, Biological replicate 2 |
| GSM1020973 |
Control Pokkali 7-day-old seedling, Biological replicate 3 |
| GSM1020974 |
Control IR29 7-day-old seedling, Biological replicate 1 |
| GSM1020975 |
Control IR29 7-day-old seedling, Biological replicate 2 |
| GSM1020976 |
Control IR29 7-day-old seedling, Biological replicate 3 |
| GSM1020977 |
3 h stress Nonabokra 7-day-old seedling, Biological replicate 1 |
| GSM1020978 |
3 h stress Nonabokra 7-day-old seedling, Biological replicate 2 |
| GSM1020979 |
3 h stress Nonabokra 7-day-old seedling, Biological replicate 3 |
| GSM1020980 |
3 h stress Pokkali 7-day-old seedling, Biological replicate 1 |
| GSM1020981 |
3 h stress Pokkali 7-day-old seedling, Biological replicate 2 |
| GSM1020982 |
3 h stress Pokkali 7-day-old seedling, Biological replicate 3 |
| GSM1020983 |
3 h stress IR29 7-day-old seedling, Biological replicate 1 |
| GSM1020984 |
3 h stress IR29 7-day-old seedling, Biological replicate 2 |
| GSM1020985 |
3 h stress IR29 7-day-old seedling, Biological replicate 3 |
| GSM1020986 |
6 h stress Nonabokra 7-day-old seedling, Biological replicate 1 |
| GSM1020987 |
6 h stress Nonabokra 7-day-old seedling, Biological replicate 2 |
| GSM1020988 |
6 h stress Nonabokra 7-day-old seedling, Biological replicate 3 |
| GSM1020989 |
6 h stress Pokkali 7-day-old seedling, Biological replicate 1 |
| GSM1020990 |
6 h stress Pokkali 7-day-old seedling, Biological replicate 2 |
| GSM1020991 |
6 h stress Pokkali 7-day-old seedling, Biological replicate 3 |
| GSM1020992 |
6 h stress IR29 7-day-old seedling, Biological replicate 1 |
| GSM1020993 |
6 h stress IR29 7-day-old seedling, Biological replicate 2 |
| GSM1020994 |
6 h stress IR29 7-day-old seedling, Biological replicate 3 |
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| Relations |
| BioProject |
PRJNA177815 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41650_RAW.tar |
121.0 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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