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Sample GSM1210853 Query DataSets for GSM1210853
Status Public on Dec 31, 2015
Title HighCO2_6H_rep3
Sample type RNA
 
Source name HighCO2_6H_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 6hr
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_6H.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 4.159903156
ATRIKEN13566 4393.639781
ATRIKEN08029 3.224152781
ATRIKEN27822 3.233402156
ATRIKEN27713 3.243757406
ATRIKEN10969 3.2574845
ATRIKEN20199 19707.4675
ATRIKEN30075 3.297218594
ATRIKEN30830 3.315151406
ATRIKEN07335 877.1480563
ATRIKEN13579 1198.141747
ATRIKEN14133 997.2944125
ATRIKEN11487 101.8154163
ATRIKEN20010 1408.667072
ATRIKEN12111 1287.887891
ATRIKEN17481 3.49185525
ATRIKEN03251 448.2505625
ATRIKEN01799 9367.18725
ATRIKEN23687 4303.441688
ATRIKEN21530 10.58168044

Total number of rows: 34262

Table truncated, full table size 830 Kbytes.




Supplementary file Size Download File type/resource
GSM1210853_252283010084_1HighCO2-6hr-3.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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