|
| Status |
Public on Feb 14, 2014 |
| Title |
Fruit of eggplant cv PPL at 0 dpa, biological replicate 1 (normalized with 20 dpa) |
| Sample type |
RNA |
| |
|
| Source name |
Fruit of eggplant cv. PPL at 0 dpa
|
| Organism |
Solanum virginianum |
| Characteristics |
tissue: fruit
age: 0 dpa
cultivar: PPL
|
| Treatment protocol |
Eggplant plants were grown under controlled conditions in glasshouse. Flowers were hand-pollinated at anthesis and samples were collected at 0, 5, 10, 20 and 50 days post anthesis (dpa). Harvested fruits were immediately frozen in liquid nitrogen and stored at -70 °C until used for total RNA extraction.
|
| Growth protocol |
Eggplant plants were grown under controlled conditions in glasshouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from eggplant fruits of different stages.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 500 ng total RNA Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix tomato Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix tomato Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.
|
| Scan protocol |
The tomato GeneChip Genome arrays were scanned on a GeneChip scanner 3000.
|
| Description |
Gene expression profiles of fruit of eggplant cv. PPL at 0 dpa, biological replicate 1.
|
| Data processing |
After scannig CEL files were analyzed using GeneSpring GX 11.5 software. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).
|
| |
|
| Submission date |
Feb 08, 2013 |
| Last update date |
Feb 14, 2014 |
| Contact name |
Padmalatha K.V. |
| E-mail(s) |
kv.padmalatha@gmail.com
|
| Phone |
09953789208
|
| Organization name |
NRCPB
|
| Department |
Plant Biotechnology
|
| Lab |
Bt.lab
|
| Street address |
Pusa campus
|
| City |
New delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110012 |
| Country |
India |
| |
|
| Platform ID |
GPL4741 |
| Series (1) |
| GSE44182 |
Transcriptome analysis of Eggplant (Solanum melongena L.) cv. PPL during fruit development and ripening. |
|
| Relations |
| Reanalysis of |
GSM1080171 |
