|
| Status |
Public on Oct 23, 2008 |
| Title |
Arabidopsis ddc-2F_Untreated plants, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Untreated Arabidopsis ddc plants
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
15-day-old plants grown on the agar plates
|
| Growth protocol |
Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes (30 plants per plastic dish) containing GM agar (0.85%) medium supplemented with 1% sucrose for 15 days under 16-h-light/8-h-dark (40-80 mmol photons m-2 sec-1) essentially as described previously (Oono et al. 2003, Plant J. 34: 868-887).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ISOGEN (Nippon Gene Co., Toyama, Japan) extraction of total RNA from untreated seedling samples was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Eight mg of total RNA per one sample was used for synthesis of double-stranded cDNA by the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix) using an oligo(dT) primer containing the T7 RNA polymerase promoter.
Biotin-labeled cRNA was generated from the cDNA by in vivo transcription using the GeneChIP IVT Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array for 18 hr at 45°C using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned at 0.7 mm resolution using the GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Gene expression data from untreated ddc plants
|
| Data processing |
For the analysis of transcriptional activities in whole genome, intensities of a total of 6.4 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 3.2 millions PM and 3.2 millions MM probes, of individual replicates for all treated and untreated samples were normalized at the same time via quantile normalization (Bolstad et al. 2003). After this normalization, intensities of all replicates representing different samples reach a common median. Files contain data of X, Y, and intensity in order. The order is same between raw data and normalized data. Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
The intensities of (PM-MM) were used in all subsequent data analyses.
|
| |
|
| Submission date |
Aug 26, 2008 |
| Last update date |
Jul 29, 2016 |
| Contact name |
Motoaki Seki |
| E-mail(s) |
motoaki.seki@riken.jp
|
| Organization name |
RIKEN CSRS
|
| Street address |
1-7-22, Suehiro-cho, Tsurumi
|
| City |
Yokohama |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10978 |
| Series (1) |
| GSE12549 |
Expression data in Arabidopsis rdr2-1 and ddc (drm1-1drm2-2cmt3-11) mutants. |
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