|
| Status |
Public on Jun 03, 2014 |
| Title |
Empty vector transformant_line Cont2-3 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis thaliana ecotype Columbia transformed with empty vector
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype/variation: Empty vector transformant
line: Cont2-3
|
| Growth protocol |
Transgenic Arabidopsis seeds were surface-sterized and sown on GM agar plates (Valvekens et al., 1988) containing 30 mg l-1 kanamycin. The plants were grown in a growth cabinet with 16 h of light illumination per day with 80 µmol m-2 s-1 at 22°C and 60% humidity. Three-week old plants were harvested from GM agar plates for microarray analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from 3-week old Arabidopsis whole plants, using Trizol reagent (Invitrogen Corp., Carlsbad, CA, USA) and further purified using an RNeasy plant mini kit (Qiagen Inc., Valencia, CA, USA) with the addition of an on-column DNase I digestion. Quality control was performed with the Agilent 2100 Bioanalyser. Ds-cDNA was synthesized using the Invitrogen Superscipt Double-Stranded cDNA Synthesis Kit.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen MS200 Microarray Scanner, following NimbleGen standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of Arabidopsis thaliana ecotype Columbia transformed with empty vector. It is the second of three biological replicates used in this experiment, each from separate cultures (line Cont2-3).
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Feb 25, 2014 |
| Last update date |
Jun 03, 2014 |
| Contact name |
Kazuya Koyama |
| E-mail(s) |
koyama@nrib.go.jp
|
| Phone |
+81-82-420-0812
|
| Organization name |
National Research Institute of Brewing
|
| Department |
Fundamental Reesearch Division
|
| Street address |
3-7-1, Kagamiyama
|
| City |
Higashi-Hiroshima |
| State/province |
Hiroshima |
| ZIP/Postal code |
739-0046 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13970 |
| Series (2) |
| GSE55318 |
Transcript data affected by constitutive expression of VvMYBPAR in Arabidopsis |
| GSE55474 |
Functional characterization of a new grapevine MYB transcription factor and regulation of proanthocyanidin biosynthesis in grapes |
|
