|
| Status |
Public on May 16, 2011 |
| Title |
Untreated Arabidopsis axe1-5 plants array R biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Untreated Arabidopsis axe1-5 plants
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genetic background: Col-0
age: 15 d
tissue: whole seedling
genotype: axe1-5
|
| 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 to fifteen 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 45 hr at 18°C using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned at 0.7 mm resolution using the GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
15-day-old plants grown on the agar plates
Gene expression data from untreated axe1-5 plants
|
| Data processing |
For the analysis of transcriptional activities in whole genome, intensities of a total of 3.2 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 1.6 millions PM and 1.6 millions MM probes, of individual replicates for all samples were normalized via quantile normalization.
The intensities of (PM-MM) were used in all subsequent data analyses.
|
| |
|
| Submission date |
Sep 02, 2010 |
| 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 |
GPL10977 |
| Series (1) |
| GSE23950 |
Expression data in Arabidopsis axe1-5 and met1-3 mutants. |
|
