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Sample GSM5625468 Query DataSets for GSM5625468
Status Public on Oct 16, 2021
Title Sf-1_high_CO2, replicate 1
Sample type RNA
 
Source name seedling, 38DAY, Sf-1, high 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 Sf-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 1.796362857
14 7.841492924
15 1.79659078
16 1.79687022
17 1.797450743
18 1.797997804
20 8.849767986
21 1.800641903
22 1.801900541
23 5.34287908
24 6.119960219
25 7.113433597
26 1.807989546
28 6.843918592
29 7.515817226
30 1.81662036
31 3.23410369
32 8.465223668
33 8.624655597
34 1.827054056

Total number of rows: 34262

Table truncated, full table size 590 Kbytes.




Supplementary file Size Download File type/resource
GSM5625468_6855-1-18.txt.gz 6.3 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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