|
Status |
Public on Jul 31, 2016 |
Title |
WT_dry_Poly (A+)_rep3 |
Sample type |
RNA |
|
|
Source name |
WT_dry_Poly (A+)
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: whole plant genotype: rdr1/2/6 treatment: drought stress
|
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 |
|