NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE7531 Query DataSets for GSE7531
Status Public on Apr 01, 2008
Title Differentially expressed genes from different developmantal stages in rice
Platform organisms Oryza sativa; Oryza sativa Japonica Group
Sample organism Oryza sativa Japonica Group
Experiment type Expression profiling by array
Summary Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892).
2: reproducibility of hybridization-1:
We made a dye-swap experiment to validate dye-effect and data reproducibility between arrays. We hybridized shoot (as control) and other developmental stage tissues. This data also indicated the diversity of gene expression profile among developmental stages.
Keywords: variety among tissues
 
Overall design organisms: Oryza sativa ssp. japonica (Nipponbare)
tissue: shoot, root, germinated seed, panicle, callus derived from more than 100 plants
hybridization : two dye method
hybridization: dye-swap experiment
replication: germinated seed, panicle, and propagated callus were replicated twice, others were not replicated.
array: 2 array per 1 experiment (total 26 arrays)
 
Contributor(s) Ooka H, Tasaki K, Yamada-Akiyama H, Lee J, Kikuchi S
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 16, 2007
Last update date Dec 06, 2012
Contact name Kouji Satoh
Organization name NARO/HARC
Street address Hitsujigaoka 1
City Sapporo
State/province Hokkaido
ZIP/Postal code 062-8555
Country Japan
 
Platforms (2)
GPL477 RICE oligo microarray ver1
GPL892 Agilent-012106 Rice Oligo Microarray G4138A (Feature Number version)
Samples (26)
GSM182350 dye-swap experiment between germination seed and shoot 1
GSM182351 dye-swap experiment between germination seed and shoot 2
GSM182352 dye-swap experiment between root and shoot 1
Relations
BioProject PRJNA99403

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE7531_RAW.tar 128.6 Mb (http)(custom) TAR (of TXT)

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