|
| Status |
Public on Jul 31, 2016 |
| Title |
rdr126_con_Poly (A-)_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
rdr126_con_Poly (A-)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole plant
genotype: Col-0
treatment: unstress condition
|
| Treatment protocol |
The plants were transferred from MS medium to plastic dish and kept for 2 hr.
|
| Growth protocol |
rdr1/2/6 (rdr1-1; rdr2-1; rdr6-15) and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2 weeks. Growth chamber was set on 22 degree, 16 light 8 dark condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole plants using Plant RNA Isolation Reagent (Life technologies). 100μg total RNA was separated to Poly (A+) RNA and Poly (A-) fractions using Ambion Poly A purist. Poly (A-) RNA sample was prepared by depleting rRNA using Invitrogen RiboMinus Plant Kit.
|
| Label |
Cy3
|
| Label protocol |
5 ng of Poly (A+) RNA fraction and 1.4 μg of Poly (A-) samples were used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).
|
| |
|
| Hybridization protocol |
600 ng of cRNAs from Poly (A+) RNA sample and 3 mg of cRNAs from Poly (A-) RNA sample were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer (Agilent), and then dried immediately by brief centrifugation.
|
| Scan protocol |
The microarray was scanned by Agilent DNA Microarray Scanner G2539A ver. C and raw data was extracted using Feature Extraction program ver 9.1.
|
| Description |
Poly (A-) RNA
|
| Data processing |
RMA normalization was performed for signals of microarray probes using limma package on R program.
|
| |
|
| Submission date |
Aug 24, 2015 |
| Last update date |
Jul 31, 2016 |
| Contact name |
Akihiro Matsui |
| E-mail(s) |
akihiro.matsui@riken.jp
|
| Phone |
+81-45-503-9587
|
| Organization name |
RIKEN
|
| Department |
Center for Sustainable Resource Science
|
| Lab |
Plant Genomic Network Research Team
|
| Street address |
1-7-22 Suehiro-cho, Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL20796 |
| Series (1) |
| GSE72309 |
Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under abiotic stress |
|
