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Sample GSM1334046 Query DataSets for GSM1334046
Status Public on Jun 03, 2014
Title Empty vector transformant_line Cont2-3
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: Cont2-3
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 second of three biological replicates used in this experiment, each from separate cultures (line Cont2-3).
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 10.585289
AT1G01020_1 6.1976295
AT1G01020_2 4.8243346
AT1G01030_1 9.450712
AT1G01040_1 11.867189
AT1G01046_1 9.629754
AT1G01050_1 12.696488
AT1G01060_1 11.521526
AT1G01060_3 5.3196287
AT1G01070_1 10.650788
AT1G01070_2 3.4411383
AT1G01073_1 3.8907385
AT1G01080_1 12.994445
AT1G01080_2 12.898137
AT1G01090_1 14.079551
AT1G01100_1 13.315553
AT1G01100_2 13.457927
AT1G01100_3 13.825242
AT1G01110_1 10.766841
AT1G01110_2 10.905247

Total number of rows: 37118

Table truncated, full table size 784 Kbytes.

Supplementary file Size Download File type/resource
GSM1334046_555898A04_Slot20_2013-04-17_532.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM1334046_555898A04_Slot20_2013-04-17_532_RMA.calls.gz 411.8 Kb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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