|
| Status |
Public on Apr 08, 2006 |
| Title |
Col-0_PsmES4326_24hpi_C_miniarray_1 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis thalia leaves, PsmES4326 treated, 24hpi
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Genotype: Col-0, Tissue: leaves, Age: 33 days post planting
|
| Biomaterial provider |
Raka M. Mitra
|
| Treatment protocol |
Individual leaves were injected in the morning using a needle-less syringe with 10E4 cfu cm-2 PsmES4326 (suspended in 5mM MgSO4) and harvested 24 hours later.
|
| Growth protocol |
Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and 75% humidity with a 12 hour day length.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Alexa555
|
| Label protocol |
Following procedure was performed with Amino Allyl MessageAmp aRNA Amplification Kit II (Ambion). First, cDNA was synthesized from 1ug of total RNA. Next, RNA was in vitro transcribed. The RNA was then labeled with Alexa555 in coupling reaction.
|
| |
|
| Hybridization protocol |
Labeled RNA was suspended in hybridization buffer (50% Formamide, 5xSSC, 0.1% SDS, 10 ug Sheared Salmon Sperm DNA (Eppendorf), 50 pmol calbation oligo, a Cy5-labeled 69mer oligonucleotide)
|
| Scan protocol |
Slide was scaneed using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.
|
| Description |
Pseudomonas syringae ES4326 inoculated, 24hpi, set C
|
| Data processing |
The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray. The residual Eij is assumed to be independent and normally distributed. Stable genes-based quantile normalization was applied when the estimated expression value in different slides was compared. Col_MgSO4_24h_C_miniarray_1, Col_MgSO4_24h_C_miniarray_2, Col_Psm_24h_C_miniarray_1, and Col_Psm_24h_C_miniarray_2 were normalized together. Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu). Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.
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| |
|
| Submission date |
Apr 07, 2006 |
| Last update date |
Apr 07, 2006 |
| Contact name |
Masanao Sato |
| Phone |
+81-564-59-5876
|
| Organization name |
National Institute for Basic Biology
|
| Lab |
Developmental Genetics
|
| Street address |
5-1 Higashiyama, Myodaiji
|
| City |
Okazaki |
| State/province |
Aichi |
| ZIP/Postal code |
444-8787 |
| Country |
Japan |
| |
|
| Platform ID |
GPL3638 |
| Series (1) |
| GSE4632 |
Evaluation of performance of Arabidopsis Pathoarray 464_001: comparison with ATH1 |
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