NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1210873 Query DataSets for GSM1210873
Status Public on Dec 31, 2015
Title HighCO2_2W_rep3
Sample type RNA
 
Source name HighCO2_2W_in_ChamberA
Organism Arabidopsis thaliana
Characteristics cultivar: Col-0; wild type
tissue: 14-d-old seedlings
exposed to: elevated (780 μmol mol-1) CO2 for 14 days
chamber id: ChamberA
Extracted molecule total 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)
Description HighCO2_2W.b1
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 Aug 18, 2013
Last update date Dec 31, 2015
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)
GSE49960 Transcriptome analysis of annotated coding genes and sORF under elevated CO2

Data table header descriptions
ID_REF
VALUE quantile normalized

Data table
ID_REF VALUE
ATRIKEN31987 15.12343409
ATRIKEN13566 4130.556219
ATRIKEN08029 23.75451719
ATRIKEN27822 4.962809344
ATRIKEN27713 18.61698375
ATRIKEN10969 7.129135
ATRIKEN20199 13087.69406
ATRIKEN30075 15.56046822
ATRIKEN30830 18.33833563
ATRIKEN07335 1116.529313
ATRIKEN13579 1122.747369
ATRIKEN14133 801.7841094
ATRIKEN11487 97.91594438
ATRIKEN20010 1152.992472
ATRIKEN12111 675.2007063
ATRIKEN17481 10.44649222
ATRIKEN03251 908.0209
ATRIKEN01799 10638.61638
ATRIKEN23687 3795.270281
ATRIKEN21530 9.130976938

Total number of rows: 34262

Table truncated, full table size 829 Kbytes.




Supplementary file Size Download File type/resource
GSM1210873_252283010080_1HighCO2-2w-3.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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