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Sample GSM1210843 Query DataSets for GSM1210843
Status Public on Dec 31, 2015
Title HighCO2_0H_rep1
Sample type RNA
 
Source name HighCO2_0H_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 0hr
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_0H.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 2.565818344
ATRIKEN13566 5413.234938
ATRIKEN08029 5.22985125
ATRIKEN27822 2.556022844
ATRIKEN27713 4.436208344
ATRIKEN10969 6.583102219
ATRIKEN20199 13353.63359
ATRIKEN30075 3.348040781
ATRIKEN30830 2.55430275
ATRIKEN07335 1069.324181
ATRIKEN13579 1028.244322
ATRIKEN14133 627.7791063
ATRIKEN11487 78.936205
ATRIKEN20010 1646.287034
ATRIKEN12111 2255.202531
ATRIKEN17481 2.942384094
ATRIKEN03251 322.00565
ATRIKEN01799 6812.574219
ATRIKEN23687 4540.281781
ATRIKEN21530 9.906649969

Total number of rows: 34262

Table truncated, full table size 830 Kbytes.




Supplementary file Size Download File type/resource
GSM1210843_252283010059_1HighCO2-0h-1r.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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