NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM266306 Query DataSets for GSM266306
Status Public on Feb 16, 2008
Title Primary root_rep_167 998_Cy3_301x002
Sample type RNA
 
Source name Maize primary root 3.5 dag
Organism Zea mays
Characteristics genotype: 301x002
Growth protocol Germination in a phytochamber at 26°C, with a 16 hours light, 8 hours dark cycle and 60% humidity in twice distilled water.
Extracted molecule polyA RNA
Extraction protocol For each biological replicate approximately 20 roots per germination roll and genotype were pooled and homogenized using the Micro-Dismembrator U (Sartorius AG, Göttingen, Germany). Isolation of total RNA with Trizol (Invitrogen, Carlsbad, CA, USA), followed by mRNA purification using Oligotex mRNA columns (Qiagen, Hilden, Germany) was performed according to the manufacturers´ instructions.
Label Cy5
Label protocol Reverse transcription of the mRNA to cDNA with concurrent incorporation of aminoallyl dUTPs as well as Cy3 and Cy5 labeling was performed according to Nakazono et al. (2003).
 
Hybridization protocol Microarray probe hybridization of spotted 12k maize cDNA microarray chips (GenII vB, GPL 1996; www.plantgenomics.iastate.edu/maizechip) representing 10,649 non-redundant gene fragments was conducted as described in Woll et al. (2005).
Scan protocol Dried slides were scanned six times with an Array Scanner (Genetic MicroSystems, USA) for each channel (Cy3 and Cy5) with laser power settings fixed at 90%. A series of up to six scans for each channel, in ascending order of PMT gain, was performed at 10 mm resolution individually adjusted to overall spot intensities per array according to Piepho et al. (2006). ImaGene software (Biodiscovery, Marina Del Rey, CA, USA) was used to quantify the spot intensities on the slides by the use of the default settings. ImaGene software (Biodiscovery, Marina Del Rey, CA, USA) was used to quantify the spot intensities on the slides by the use of the default settings.
Description slide 998
998_Cy3_301x002
Data processing The experimental design for the microarray experiments was described in Keller et al. (2005). To combine data from different scanning intensities, a nonlinear latent regression model was applied (Piepho et al., 2006). After combining the signals of different scans, a loess regression was performed. To account for differences between arrays the median absolute deviations (MAD) of the slides were normalized. The normalized data was analysed by a linear mixed model for every gene. Effects that occur during hybridization (genotype, dye, slide) were considered as well as temporal and spatial effects that might affect the genetic material during cultivation in the phytochamber (Keller et al., 2005). The unbalancedness of the design was accounted for by the mixed model analysis. Pairwise contrasts between genotypes were estimated. Furthermore, linear contrasts between hybrid and parental mean were determined. The p-values of these contrasts based on Wald tests were adjusted for multiple testing by controlling the false discovery rate (FDR) at 5% using the procedure of Benjamini and Hochberg (1995). The analyses for this paper were generated using SAS software, Version 9. Linear model analyses were done by PROC MIXED, while the FDR adjustment was performed by PROC MULTTEST.
 
Submission date Feb 15, 2008
Last update date Feb 15, 2008
Contact name Frank Hochholdinger
E-mail(s) [email protected]
Phone 0049 228 73 60334
Fax 0049 228 73 60333
URL http://www.lwf.uni-bonn.de/institute/inres/institut/crop-functional-genomics/
Organization name University of Bonn
Department INRES - Crop Functional Genomics
Lab Hochholdinger
Street address Katzenburgweg 1a
City Bonn
State/province BW
ZIP/Postal code 53115
Country Germany
 
Platform ID GPL1996
Series (1)
GSE10539 Maize primary roots: inbred lines vs. hybrids

Data table header descriptions
ID_REF
VALUE normalized log2 values

Data table
ID_REF VALUE
1 0
2 0
3 0
4 0
5 0
6 0
7 2.714853686
8 9.49420627
9 9.565856831
10 9.555371574
11 9.765592313
12 9.400511444
13 9.41074151
14 9.353227352
15 9.481016706
16 9.945664847
17 10.04457736
18 10.01507705
19 9.519501117
20 0

Total number of rows: 12160

Table truncated, full table size 196 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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