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Sample GSM1334043 Query DataSets for GSM1334043
Status Public on Jun 03, 2014
Title MYBPAR expressing Arabidopsis_line PAR9-2
Sample type RNA
 
Source name Arabidopsis thaliana ecotype Columbia transformed with 35S::VvMYBPAR construct
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia
genotype/variation: Plant transformed with 35S::VvMYBPAR construct
line: PAR9-2
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 www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen MS200 Microarray Scanner, following NimbleGen standard operating protocol. See www.nimblegen.com.
Description This sample is of Arabidopsis thaliana ecotype Columbia transformed with 35S::VvMYBPAR. It is the second of three biological replicates used in this experiment, each from separate cultures (line PAR9-2).
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
E-mail(s) koyama@nrib.go.jp
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
ID_REF
VALUE log2 transformed expression values

Data table
ID_REF VALUE
AT1G01010_1 10.75863
AT1G01020_1 6.2788954
AT1G01020_2 5.904159
AT1G01030_1 8.796917
AT1G01040_1 11.658887
AT1G01046_1 9.420362
AT1G01050_1 13.048943
AT1G01060_1 7.5287743
AT1G01060_3 4.213884
AT1G01070_1 9.831653
AT1G01070_2 3.9296112
AT1G01073_1 3.4465075
AT1G01080_1 13.310136
AT1G01080_2 13.297112
AT1G01090_1 14.251927
AT1G01100_1 13.633364
AT1G01100_2 13.70774
AT1G01100_3 13.972187
AT1G01110_1 10.590883
AT1G01110_2 10.90304

Total number of rows: 37118

Table truncated, full table size 784 Kbytes.




Supplementary file Size Download File type/resource
GSM1334043_555898A07_Slot20_2013-04-17_532.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM1334043_555898A07_Slot20_2013-04-17_532_RMA.calls.gz 414.4 Kb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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