NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1314352 Query DataSets for GSM1314352
Status Public on Nov 30, 2014
Title newly synthetic triploid_rep2
Sample type RNA
 
Source name S0_SynT124, replicate 2
Organism Triticum dicoccon x Aegilops tauschii subsp. strangulata
Characteristics tissue: leaf
age: two leaves seedling
Treatment protocol Ttriploid embryos were rescued 2 weeks later after pollination. Embryos were placed petridishes with half strength of Murashige & Skoog culture medium (Inagaki et al. 1998) in growth chamber which is maintained at 20℃, 12-h light/12-h dark (5000 lux). Chromosome-doubled hexaploid plants obtained by self-pollination of colchicine treated (0.2% in a 2% DMSO solution) of triploid plants.
Growth protocol All plants were grown in growth chamber controlled by at 22℃, relative humidity 40%, in 16 h length with 6000 lux (64,560 fc) and 8 h dark day cycles.
Extracted molecule total RNA
Extraction protocol Total RNA of each line was extracted using Plant RNeasy Mini Kit (Qiagen) according to the manufacturer’s method.
Label Cy3
Label protocol Extracted RNAs (500ng) were labelled using the Agilent Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies) with cyamine 3-cytidine 5C-triphosphate (CTP).
 
Hybridization protocol Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.
Scan protocol After washing, signal intensities were immediately detected by Feature Extraction software (Agilent Technologies). Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is XDR Hi 100% and XDR Li 10%).
Description Gene expression of newly synthetic triploid
Data processing Signal intensities were detected from the obtained digital images with Feature Extraction software 9.5 (Agilent Technologies). Fluorescence intensities were analysed with GeneSpring GX v12.6 (Agilent Technologies). Raw data set (raw signal intensity > 1.0 threshold) was transformed to log scale at base 2. Normalization was performed with GeneSpring.
 
Submission date Jan 24, 2014
Last update date Jan 12, 2015
Contact name Yeonju Jung
E-mail(s) congdan2@gmail.com
Organization name Kihara Institute for Biological Research
Department Yokohama City University
Lab Plant Genome Science
Street address Maioka-cho 641-12
City Yokohama
State/province Kanagawa
ZIP/Postal code 244-0813
Country Japan
 
Platform ID GPL9805
Series (1)
GSE54398 Expression profiles of synthetic wheat lines and their parents during amphidiploidization

Data table header descriptions
ID_REF
VALUE Normalized (processed) signal intensity

Data table
ID_REF VALUE
12 -0.1469512
16 0.6170964
21 -0.14557219
22 0.11101627
23 1.6799803
25 0.15024948
27 -0.53334236
28 0.5545685
31 0.5251398
33 -0.40509033
34 -0.27670336
35 0.14600372
38 -0.065312386
39 0.41154718
42 0.40357828
43 0.3447585
44 0.38401222
46 0.300148
47 -0.045497894
48 -0.7025819

Total number of rows: 20802

Table truncated, full table size 346 Kbytes.




Supplementary file Size Download File type/resource
GSM1314352_G1_3x_2.txt.gz 5.3 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap