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Sample GSM242958 Query DataSets for GSM242958
Status Public on Nov 15, 2007
Title Mock day 3 (day3E2)
Sample type RNA
 
Source name inflorescence tips, 3 days after mock-treatment
Organism Arabidopsis thaliana
Characteristics ap1-1 and cal-1, 35S:AGGR background, L-er accession, grown in controlled environment room at 18 C, 16h light/8h dark
Treatment protocol Dexamethasone (Sigma, stock solution 10 mM in ethanol) was used at a final concentration of 10 μM in Silwet L-77 0.015%, applied directly on the inflorescence tips; for mock treatments, the solution contained the same amount of ethanol (0.1%) and Silwet L-77. After treatment, RNA was extracted from inflorescence apices and stored at -70 C until activation of AGGR was confirmed (2 weeks later).
Growth protocol Plants were grown on a mix of vermiculite:soil:sand at 18°C with 16 hours light/8 hours dark cycles.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRI reagent (Sigma) according to the manufacturer’s instructions. For array hybridisation, the RNA was cleaned up with RNeasy columns (Qiagen) and precipitated to increase final concentration.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 50C on GeneChip Arabidopsis ATH1 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description mock treatment was ethanol 0.1%, Silwet L-77 0.015%
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. To calculate p-values for expression changes after steroid treatmen at each time point, the Wilcoxon signed-rank test was applied to each of the four pairwise combinations of steroid-treated X control sample, using MAS 5.0.
 
Submission date Nov 14, 2007
Last update date Aug 28, 2018
Contact name Robert Sablowski
E-mail(s) robert.sablowski@jic.ac.uk
Phone +44 1603 450530
Organization name JIC
Department CDB
Street address The John Innes Centre
City NORWICH
State/province Norfolk
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platform ID GPL198
Series (1)
GSE9605 Target genes of AGAMOUS during early flower development in Arabidopsis
Relations
Reanalyzed by GSE118579
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 93.2 P 0.000054
AFFX-BioB-M_at 142.1 P 0.000001
AFFX-BioB-3_at 111.5 P 0.000909
AFFX-BioC-5_at 279 P 0.000429
AFFX-BioC-3_at 183 P 0.000016
AFFX-BioDn-5_at 132.7 P 0
AFFX-BioDn-3_at 1261.2 P 0
AFFX-CreX-5_at 1902.9 P 0
AFFX-CreX-3_at 3886 P 0.000031
AFFX-DapX-5_at 0.3 A 0.036913
AFFX-DapX-M_at 2.9 A 0.849661
AFFX-DapX-3_at 1 A 0.5
AFFX-LysX-5_at 2.6 A 0.430643
AFFX-LysX-M_at 1.9 A 0.5
AFFX-LysX-3_at 0.5 A 0.194828
AFFX-PheX-5_at 0.9 A 0.108118
AFFX-PheX-M_at 0.8 A 0.5
AFFX-PheX-3_at 2.9 A 0.221792
AFFX-ThrX-5_at 5.7 A 0.494638
AFFX-ThrX-M_at 1 A 0.378604

Total number of rows: 22810

Table truncated, full table size 544 Kbytes.




Supplementary file Size Download File type/resource
GSM242958.CEL.gz 3.2 Mb (ftp)(http) CEL
GSM242958.EXP.gz 461 b (ftp)(http) EXP
Raw data provided as supplementary file
Processed data included within Sample table

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