|
| Status |
Public on Aug 18, 2006 |
| Title |
ndr1-1blind_Pst-avrRpt2_6h_set2 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis thalia leaves, Pseudomonas syringae pv. tomato DC3000 avrRpt2 injected, 6h
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Genotype: ndr1-1blind, Tissue: leaves, Age: 4 weeks post planting
|
| Biomaterial provider |
Masanao Sato
|
| Treatment protocol |
Individual leaves were injected in the morning using a needle-less syringe with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2 and harvested 6h 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.
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| |
|
| 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 scaned using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.
|
| Description |
ndr1-1blind infected with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2, harvested 6h after injection in set2 experiment, 6h, set2
|
| 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 for slide-to-slide comparisons. Col-0_Pst-avrRpt2_6h_set1, rps2-101C_Pst-avrRpt2_6h_set1, ndr1-1_Pst-avrRpt2_6h_set1, ndr1-1blind_Pst-avrRpt2_6h_set1, Col-0_Pst-avrRpt2_6h_set2, rps2-101C_Pst-avrRpt2_6h_set2, ndr1-1_Pst-avrRpt2_6h_set2, 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 |
Aug 02, 2006 |
| Last update date |
Aug 18, 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) |
| GSE5308 |
Evaluation of the performance of the Arabidopsis Pathoarray 464_001: an example of detailed analysis of mutants |
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