NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1859871 Query DataSets for GSM1859871
Status Public on Jul 31, 2016
Title rdr126_con_Poly (A-)_rep3
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

Data table header descriptions
ID_REF
VALUE Log2 Normalized signal intensity

Data table
ID_REF VALUE
AT5G38830 10.5
AT3G30655 9.2
AT5G62670 11.3
AT1G47317 8.2
AT2G15815 7.7
AT4G19035 9.4
AT_2_-_0_3373939-3374124 12.0
Group5692 9.3
Group6436 10.3
AT_3_+_2_13108191-13108343 9.7
AT1G35745 9.1
AT_5_-_0_2299090-2299230 9.2
AT2G39340 8.5
AT3G46710 9.8
Group786 8.9
AT1G31350 9.2
AT4G21215 9.4
AT_2_+_1_6838904-6839089 9.6
AT5G05850 11.5
AT3G42313 7.8

Total number of rows: 52586

Table truncated, full table size 864 Kbytes.




Supplementary file Size Download File type/resource
GSM1859871_rdr126_0h_nonPolyA_3_US45103077_253459210021_S01_GE1_107_Sep09_2_2.txt.gz 7.6 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap