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Sample GSM1210863 Query DataSets for GSM1210863
Status Public on Dec 31, 2015
Title HighCO2_3D_rep1
Sample type RNA
 
Source name HighCO2_3D_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 3 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_3D.a1
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 2.401701781
ATRIKEN13566 5050.675688
ATRIKEN08029 2.397225094
ATRIKEN27822 2.396188156
ATRIKEN27713 2.838879563
ATRIKEN10969 8.321600594
ATRIKEN20199 17544.50681
ATRIKEN30075 2.396327031
ATRIKEN30830 2.488403375
ATRIKEN07335 853.4297938
ATRIKEN13579 1054.197541
ATRIKEN14133 537.3102563
ATRIKEN11487 78.52746906
ATRIKEN20010 1545.54865
ATRIKEN12111 2404.60975
ATRIKEN17481 2.725981344
ATRIKEN03251 571.8812281
ATRIKEN01799 6409.947563
ATRIKEN23687 3918.582531
ATRIKEN21530 11.52958731

Total number of rows: 34262

Table truncated, full table size 829 Kbytes.




Supplementary file Size Download File type/resource
GSM1210863_252283010059_3HighCO2-3d-1.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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