GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1334047 Query DataSets for GSM1334047
Status Public on Jun 03, 2014
Title Empty vector transformant_line Cont5-1
Sample type RNA
Source name Arabidopsis thaliana ecotype Columbia transformed with empty vector
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia
genotype/variation: Empty vector transformant
line: Cont5-1
Growth protocol Transgenic Arabidopsis seeds were surface-sterized and sown on GM agar plates (Valvekens et al., 1988) containing 30 mg l-1 kanamycin. The plants were grown in a growth cabinet with 16 h of light illumination per day with 80 µmol m-2 s-1 at 22°C and 60% humidity. Three-week old plants were harvested from GM agar plates for microarray analysis.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from 3-week old Arabidopsis whole plants, using Trizol reagent (Invitrogen Corp., Carlsbad, CA, USA) and further purified using an RNeasy plant mini kit (Qiagen Inc., Valencia, CA, USA) with the addition of an on-column DNase I digestion. Quality control was performed with the Agilent 2100 Bioanalyser. Ds-cDNA was synthesized using the Invitrogen Superscipt Double-Stranded cDNA Synthesis Kit.
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See
Scan protocol Scanning was performed by NimbleGen MS200 Microarray Scanner, following NimbleGen standard operating protocol. See
Description This sample is of Arabidopsis thaliana ecotype Columbia transformed with empty vector. It is the third of three biological replicates used in this experiment, each from separate cultures (line Cont5-1).
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).
Submission date Feb 25, 2014
Last update date Jun 03, 2014
Contact name Kazuya Koyama
Phone +81-82-420-0812
Organization name National Research Institute of Brewing
Department Fundamental Reesearch Division
Street address 3-7-1, Kagamiyama
City Higashi-Hiroshima
State/province Hiroshima
ZIP/Postal code 739-0046
Country Japan
Platform ID GPL13970
Series (2)
GSE55318 Transcript data affected by constitutive expression of VvMYBPAR in Arabidopsis
GSE55474 Functional characterization of a new grapevine MYB transcription factor and regulation of proanthocyanidin biosynthesis in grapes

Data table header descriptions
VALUE log2 transformed expression values

Data table
AT1G01010_1 10.709766
AT1G01020_1 6.4994836
AT1G01020_2 5.6734605
AT1G01030_1 9.490777
AT1G01040_1 11.706852
AT1G01046_1 9.783671
AT1G01050_1 13.051469
AT1G01060_1 13.042276
AT1G01060_3 5.3959193
AT1G01070_1 10.829438
AT1G01070_2 4.0355535
AT1G01073_1 3.320369
AT1G01080_1 12.914111
AT1G01080_2 12.860282
AT1G01090_1 14.296362
AT1G01100_1 13.388752
AT1G01100_2 13.58573
AT1G01100_3 13.986714
AT1G01110_1 10.684261
AT1G01110_2 11.006493

Total number of rows: 37118

Table truncated, full table size 784 Kbytes.

Supplementary file Size Download File type/resource
GSM1334047_555898A10_Slot20_2013-04-17_532.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM1334047_555898A10_Slot20_2013-04-17_532_RMA.calls.gz 413.3 Kb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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