|
| Status |
Public on Sep 30, 2012 |
| Title |
Root_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
treatment group: tissue
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Approximately 500 μg of total RNA was three times extracted from each sample using TRIzol (Invitrogen).
|
| Label |
Cy3
|
| Label protocol |
cRNA amplification and fluorescence labeling were performed using the Agilent Low RNA Input Linear Amplification Kit (Agilent Technology, Tokyo, Japan) according to the manufacturer's protocol. A primer containing poly dT and a T7 polymerase promoter was annealed to the poly A+ RNA. First and second strands of cDNA were reverse transcribed from 500 ng total RNA using MMLV-RT enzyme. Cyanine 3- labeled cRNA was synthesized using T7 RNA polymerase. Labeled cRNA was purified by RNeasy Mini Kit (Qiagen, Tokyo, Japan).
|
| |
|
| Hybridization protocol |
Hybridization was performed using the in situ Hybridization Kit Plus (Agilent Technologies, Tokyo, Japan)
|
| Scan protocol |
Hybridized and washed material on each glass slide was scanned by an Agilent G2505 B DNA microarray scanner (Agilent Technologies)
|
| Data processing |
Data analysis was performed by Feature Extraction and Image Analysis software (Agilent Technologies, Tokyo, Japan). The array intensities were processed using the Bioconductor (www.bioconductor.org) affy package in the R software environment (www.r-project.org). Hybridization intensities in our arrays were simply normalized among different arrays by quantile normalization.
|
| |
|
| Submission date |
Dec 06, 2011 |
| Last update date |
Sep 30, 2012 |
| Contact name |
Kousuke Hanada |
| E-mail(s) |
kohanada@bio.kyutech.ac.jp
|
| Organization name |
Kyushu Institute Technology
|
| Department |
Department of Bioscience and Bioinformatics
|
| Street address |
680-4 Kawazu
|
| City |
Iizuka |
| State/province |
Fukuoka |
| ZIP/Postal code |
820-8502 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14937 |
| Series (1) |
| GSE34188 |
Transcriptome analysis of annotated coding genes and sORF in 16 organs and 17 environmental conditions at A. thaliana |
|
