|
| Status |
Public on Oct 01, 2015 |
| Title |
Global gene expression signatures in high temperature stressed sweet potato fibrous root |
| Sample type |
RNA |
| |
|
| Source name |
Fibrous roots from high temperature stressed sweet potato plants
|
| Organism |
Ipomoea batatas |
| Characteristics |
treatment: high temperature stressed
tissue: Fibrous roots
age: 30 days old
|
| Treatment protocol |
One set of 30 plants were kept in ambient conditions and another set of 30 plants were used as control. Ambient temperature conditions were 30oC ± 2oC during day time and 23oC ± 1oC during night time. Another set of 21 days old 30 plants were subjected to high temperature stress for 7 hours daily at 40oC ±2oC during day time and 23 oC ± 1oC during night time for 7 days.
|
| Growth protocol |
Sweet potato plants of variety Sree Arun were grown in earthen pots of 7 kg soil holding capacity and irrigated daily. Nitrogen (0.6 g urea), phosphorous (0.3 g P2O5) and potassium (0.6 g K2O ) fertilizers were added one week after planting. Plants were illuminated for 12 hours per day under 700 µ mol m2 h-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the leaf, fibrous root and tuberous root by the method as described by Chomczynski, P. and Sacchi, N. 1987. Anal. Biochem 162:156. Total intact high quality RNA were extracted from young newly emerging tender leaves, fibrous roots and tuber forming roots harvested from 30 days old sweet potato plants grown in ambient temperature and from plants subjected to high temperature stress.
|
| Label |
Cy3
|
| Label protocol |
The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop.
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| |
|
| Hybridization protocol |
600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5242).
|
| Scan protocol |
Slides were then scanned on a G2505C scanner (Agilent Technologies)
|
| Description |
Global gene expression fibrous root after 7 hours high tempersture (day 40oC; night 23oC) treatment for 7 days
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software and Analyis perfomed using background subtracted and spatially detrended Processed Signal intensities and Percentile Shift Normalization
|
| |
|
| Submission date |
Oct 29, 2013 |
| Last update date |
Oct 01, 2015 |
| Contact name |
Genotypic technology |
| E-mail(s) |
sudha.rao@genotypic.co.in
|
| Organization name |
Genotypic Technology
|
| Street address |
259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE
|
| City |
Bangalore |
| State/province |
Karnataka |
| ZIP/Postal code |
560094 |
| Country |
India |
| |
|
| Platform ID |
GPL17857 |
| Series (1) |
| GSE51862 |
Analysis of global gene expression signatures in sweet potato as affected by temperature stress |
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