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Sample GSM5625466 Query DataSets for GSM5625466
Status Public on Oct 16, 2021
Title Col-0_ambient_CO2, replicate 1
Sample type RNA
 
Source name seedling, 38DAY, Col-0, ambient CO2 condition, replicate 1
Organism Arabidopsis thaliana
Characteristics tissue: seedling
age: 38 day
Growth protocol A. thaliana were grown under ambient and elevated CO2 conditions (800 μmol mol-1) for 38 days and harvested for the analysis. The ambient CO2 condition was mostly kept as 380–400 μmol mol-1. Growth temperature and humidity were set to 20 °C and 60 %. The photoperiod was 10 h day-1 (130 μmol m-2 s-1 for a total of 9 h and 660 μmol m-2 s-1 for 1 h in the midphotoperiod). Metal-halide lamps (MF400L-J2/BU-PS; Mitsubishi/Osram, Yokohama, Japan) were used as the growth light sources.
Extracted molecule total RNA
Extraction protocol In each condition, total RNA was prepared using TRIzol reagent (Life Technologies Japan, Tokyo, Japan) and 800 ng RNA was used for the microarray analysis.
Label Cy3
Label protocol cRNA amplification and fluorescence labelling with Cy3 were performed using the Agilent One-Color Low RNA Input Linear Amplification Kit (Agilent Technologies, Tokyo, Japan).
 
Hybridization protocol Hybridization was performed using the in situ Hybridization Kit Plus.
Scan protocol Microarrays were scanned using an Agilent G2505 B Microarray Scanner. Microarray images were analyzed and data extracted using Feature Extraction 9.1 software (Agilent Technologies).
Description Gene expression in Col-1
Data processing The microarray signal intensities were processed using the Bioconductor (www.bioconductor.org) package in the R software environment (www.r-project.org, version 3.5.2).
 
Submission date Oct 14, 2021
Last update date Oct 16, 2021
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 GPL30841
Series (1)
GSE185907 Stimulations of the growth rate in elevated CO2 condition were observed in over-expression or RNA interference lines of genes identified by intraspecific variation analyses.

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
13 1.553580534
14 7.768640272
15 2.692650228
16 1.54518671
17 1.543173316
18 1.541549145
20 8.715240613
21 1.538925315
22 1.538694152
23 5.491639857
24 6.269995501
25 6.887530224
26 1.541169778
28 6.826221527
29 7.547194146
30 1.548148082
31 1.852023712
32 8.905563275
33 8.659495903
34 1.559171459

Total number of rows: 34262

Table truncated, full table size 590 Kbytes.




Supplementary file Size Download File type/resource
GSM5625466_22681-4-27.txt.gz 6.3 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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