|
| Status |
Public on May 24, 2016 |
| Title |
control cultivar 3 vs treatment cultivar 3 replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Seedlings grown in climate chambers
|
| Organism |
Zea mays |
| Characteristics |
variety: PR39B29
treatment: control
tissue: primary root
age: 8 days post-germination
variety: PR39B29
treatment: cold-treated
age: 8 days post-germination
|
| Growth protocol |
In growth chambers: Control (18°C/16h, 12°C/6h, dark) - Cold treatment (12°C/16h, 6°C/8h, dark)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extraced from roots with a Qiagen Rneasy© Plant Mini Kit
|
| Label |
Cy3
|
| Label protocol |
RNA samples were labelled with Cy3/Cy5 fluorophores by the manufacturer
|
| |
|
| Channel 2 |
| Source name |
Seedlings grown in climate chambers
|
| Organism |
Zea mays |
| Characteristics |
tissue: primary root
|
| Growth protocol |
In growth chambers: Control (18°C/16h, 12°C/6h, dark) - Cold treatment (12°C/16h, 6°C/8h, dark)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extraced from roots with a Qiagen Rneasy© Plant Mini Kit
|
| Label |
Cy5
|
| Label protocol |
RNA samples were labelled with Cy3/Cy5 fluorophores by the manufacturer
|
| |
|
| |
| Hybridization protocol |
Hybridization was carried out according to a direct comparative loop design
|
| Scan protocol |
Image acquisition was performed with a GenePix® scanner and quantified with the in-built software
|
| Description |
Biological replicate 2 of 3. Control cultivar 3 was hybrized with the treatment cultivar 3 on the spotted oligo-array as a part of a microarray loop design.
|
| Data processing |
Data were background corrected with the minimum method, print-tip lowess (within-array) normalized and scaled (between-array) from log2 of processed red signal/processed green signal
Quality check was performed with the MapMan Robin software. Data were processed and analysed with the web-based application CarmaWeb
Data Analysis: The normalized intensities within an array and between replicates were averaged to one single value per gene. Differentially expressed genes were determined with the limma paired moderate t-test. Adjusted p-values were generated according to the Benjamini and Hochberg (BH) method.
|
| |
|
| Submission date |
Aug 28, 2015 |
| Last update date |
May 25, 2016 |
| Contact name |
Mauro Di Fenza |
| E-mail(s) |
mauro.difenza@gmail.com
|
| Organization name |
University College Dublin
|
| Street address |
Belfield
|
| City |
Dublin |
| ZIP/Postal code |
4 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL6438 |
| Series (1) |
| GSE72508 |
Maize (Zea mays): control vs cold stress |
|
