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Sample GSM2977322 Query DataSets for GSM2977322
Status Public on Nov 13, 2018
Title Col-0_8 h mock plate_biological rep1
Sample type RNA
 
Source name Col-0, whole seedlings, 8 h mock
Organism Arabidopsis thaliana
Characteristics genotype: Col-0 wild-type
tissue: Whole seedlings
developmental stage: 2 weeks after germination
treatment: 8 h mock (1/2MS)
Treatment protocol For osmotic stress treatment, two-week old seedlings were transferred onto 1/2MS infused by PEG8000 (-1.2 MPa) for 8 h under continuous light conditions.
Growth protocol Seeds were germinated and the seedlings were grown aseptically on solid 1/2MS media plus 1% sucrose at 23C under long-day (16 h light / 8 h darkness) photoperiodic conditions.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from three biological replicates by using the Plant RNA Purification Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions
Label Cy3
Label protocol Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)
 
Hybridization protocol 600 ng of cRNAs were hybridized to the microarray (GPL20796) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer (Agilent), and then dried immediately by brief centrifugation.
Scan protocol The microarray chips were scanned by Agilent DNA Microarray Scanner G2505B and raw data was extracted using Feature Extraction program ver 9.1.
Data processing Image data were normalized by RMA statistical algorithms for signals of microarray probes using limma package (Ritchie et al., 2015) on R 3.4.0. program.
 
Submission date Feb 02, 2018
Last update date Nov 13, 2018
Contact name Shunsuke Watanabe
E-mail(s) shunsuke.watanabe@riken.jp
Phone +81-45-503-9664
Organization name RIKEN
Department Center for Sustainable Resource Science
Lab Dormancy and Adaptation Research Unit
Street address 1-7-22 Suehiro-cho, Tsurumi-ku
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL20796
Series (1)
GSE110079 Comparative analysis of transcriptome profiles between wild-type Arabidopsis and two ABA deficit mutants aba3-1 and aba2-2 in osmotic stress conditions

Data table header descriptions
ID_REF
VALUE Log2 RMA signal intensity

Data table
ID_REF VALUE
AT1G01010 7.83413357
AT1G01020 10.01019115
AT1G01030 7.095712921
AT1G01040 10.63662029
AT1G01046 4.685843739
AT1G01050 12.58297551
AT1G01060 5.269986977
AT1G01070 7.003776516
AT1G01073 5.154343408
AT1G01080 10.88160425
AT1G01090 13.15577167
AT1G01100 14.96528962
AT1G01110 7.876786033
AT1G01115 5.021230569
AT1G01120 12.01798354
AT1G01130 9.19164723
AT1G01140 9.396609424
AT1G01150 4.629483038
AT1G01160 8.629187413
AT1G01170 8.843578964

Total number of rows: 52642

Table truncated, full table size 1255 Kbytes.




Supplementary file Size Download File type/resource
GSM2977322_US45103077_253459210097_S01_GE1_107_Sep09_1_1.txt.gz 7.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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