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Sample GSM1210872 Query DataSets for GSM1210872
Status Public on Dec 31, 2015
Title HighCO2_2W_rep2
Sample type RNA
 
Source name HighCO2_2W_in_ChamberB
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: ChamberB
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.a2
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 2.468213781
ATRIKEN13566 3940.353219
ATRIKEN08029 2.489190781
ATRIKEN27822 2.500994625
ATRIKEN27713 2.512898875
ATRIKEN10969 2.526239531
ATRIKEN20199 10259.78566
ATRIKEN30075 2.569513125
ATRIKEN30830 2.586662844
ATRIKEN07335 839.6683
ATRIKEN13579 983.1103
ATRIKEN14133 585.5970563
ATRIKEN11487 32.36787188
ATRIKEN20010 1875.634331
ATRIKEN12111 791.0225625
ATRIKEN17481 2.727939406
ATRIKEN03251 462.204675
ATRIKEN01799 8608.054906
ATRIKEN23687 4734.818313
ATRIKEN21530 15.67494

Total number of rows: 34262

Table truncated, full table size 829 Kbytes.




Supplementary file Size Download File type/resource
GSM1210872_252283010081_4HighCO2-2w-2.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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