NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM154953 Query DataSets for GSM154953
Status Public on Feb 15, 2007
Title Leaf_DMSO-treatment_120min_replicate 3
Sample type RNA
 
Source name Oryza sativa leaf, DMSO-control, 120 min
Organism Oryza sativa
Characteristics Oryza sativa L. cv Nipponbare, Tissue: root, Age: two weeks after germination
Treatment protocol Third leaves, which were cut at the lamina joint with a razor blade in water, were excised from the two-week-old seedlings and immediately dipped in distilled water containing 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 120 min, harvested and stored at -80°C until the RNA was extracted.
Growth protocol Rice (Oryza sativa L. cv Nipponbare) seeds were sterilized with 70 % ethanol for 1 min and then with 2 % (w/v) sodium hypochlorite for 15 min, soaked in distilled water at 30°C for 1 d and 30 germinated seeds were transferred to a nylon net floating on tap water that had been adjusted to pH 5.5. Seedlings were grown for 2-weeks in an environment-controlled greenhouse with a photoperiod of 12 h light (30°C)/12 h dark (25°C).
Extracted molecule total RNA
Extraction protocol Total RNA was prepared with the RNeasy plant Mini Kit (Qiagen).
Label biotin
Label protocol Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.
 
Hybridization protocol standard Affymetrix procedures
Scan protocol standard Affymetrix procedures
Description Publication: Naoya Hirose, Nobue Makita, Mikiko Kojima, Tomoe Kamada-Nobusada and Hitoshi Sakakibara (2007) Over-expression of a Type-A Response Regulator Alters Rice Morphology and Cytokinin Metabolism. Plant Cell Physiology, 48: in press.
Data processing GCOS1.2
 
Submission date Jan 12, 2007
Last update date Feb 15, 2007
Contact name Hitoshi Sakakibara
E-mail(s) sakaki@riken.jp
Phone 81-45-503-9576
Fax 81-45-503-9609
Organization name RIKEN
Department Plant Science Center
Lab Biodynamics Research Team
Street address 1-7-22 Suehiro, Tsurumi
City Yokohama
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL2025
Series (2)
GSE6719 Cytokinin responsive genes in rice
GSE6737 Over-expression of a Type-A Response Regulator Alters Rice Morphology and Cytokinin Metabolism

Data table header descriptions
ID_REF
VALUE GCOS-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
Detection p-value 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL Detection p-value
AFFX-BioB-5_at 301.9 P 0.000662
AFFX-BioB-M_at 352.7 P 0.000095
AFFX-BioB-3_at 306 P 0.000052
AFFX-BioC-5_at 1058.4 P 0.000044
AFFX-BioC-3_at 982.9 P 0.000044
AFFX-BioDn-5_at 2014 P 0.000044
AFFX-BioDn-3_at 3994.2 P 0.000044
AFFX-CreX-5_at 13778.3 P 0.000052
AFFX-CreX-3_at 15850 P 0.000044
AFFX-DapX-5_at 17.8 A 0.327079
AFFX-DapX-M_at 6.9 A 0.425962
AFFX-DapX-3_at 19.4 A 0.175328
AFFX-LysX-5_at 3.4 A 0.737173
AFFX-LysX-M_at 27.4 A 0.51489
AFFX-LysX-3_at 11.6 A 0.340661
AFFX-PheX-5_at 2.4 A 0.772364
AFFX-PheX-M_at 1.3 A 0.981719
AFFX-PheX-3_at 4.4 A 0.937071
AFFX-ThrX-5_at 3.1 A 0.957038
AFFX-ThrX-M_at 10.5 A 0.737173

Total number of rows: 57381

Table truncated, full table size 1956 Kbytes.




Supplementary file Size Download File type/resource
GSM154953.CEL.gz 4.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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