|
| Status |
Public on Jan 15, 2012 |
| Title |
R_solanacearum_GMI1000_28C_CPG_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Ralstonia solanacearum GMI1000, CPG, 28 C
|
| Organism |
Ralstonia pseudosolanacearum GMI1000 |
| Characteristics |
genotype: Wild Type
|
| Growth protocol |
Ralstonia solanacearum strain GMI1000 was grown to mid-log phase (~6x108 cfu ml-1) at 28 °C or in 20 °C in rich CPG medium or harvested from plants showing early symptoms of wilt with stems colonization of 1x108 cfu g-1 to1x109 cfu g-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the hot-phenol method (Jahn et al 2008) followed by 4 DNA digestion steps. RNA concentration and quality was assessed using Nanodrop and Agilent 2100 bioanalyzer (Bioanalyzer is not accurate for measuring concentration) at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed following Nimblegens standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA) following Nimblegen's standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA) following Nimblegen's standard operating protocol.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), without background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Nov 14, 2011 |
| Last update date |
Jan 15, 2012 |
| Contact name |
Lavanya Babujee |
| E-mail(s) |
[email protected]
|
| Organization name |
UW-Madison
|
| Street address |
Department of Plant Pathology
|
| City |
Madison |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL14878 |
| Series (2) |
| GSE33657 |
Expression analysis of Ralstonia solanacearum strain GMI1000 at 20°C and 28°C in rich medium (CPG) and in planta |
| GSE33662 |
Ralstonia solanacearum_GMI1000 and UW551_20 C and 28 C. |
|
