|
| Status |
Public on Dec 31, 2010 |
| Title |
3/2 MM2 |
| Sample type |
RNA |
| |
|
| Source name |
Pseudomonas syringae pv. tomato DC3000.
|
| Organism |
Pseudomonas syringae pv. tomato str. DC3000 |
| Characteristics |
strain: DC3000
mutant: PSPTO_2222-2223 deletion
media: MM
|
| Growth protocol |
Grown in KB (King et al., 1954) to ~0.7x109 cfu/mL. The bacteria were centrifuged, washed twice with MM (Huynh et al., 1989), and resuspended in MM to 3x108 cfu/mL. The bacteria were cultured in MM for 6 h before being harvested for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a modified hot phenol procedure (Aiba et al. 1981), then purified by using RNeasy Midi kit following the manufacture instruction (Qiagen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.
|
| |
|
| Hybridization protocol |
According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.
|
| Scan protocol |
According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.
|
| Description |
Gene expression data from DC3000 PSPTO_2222-2223 deletion mutant strains when grown in MM at 6hr(King et al., 1954).
|
| Data processing |
For each probe on the array, the median signal intensity was calculated using the NimbleGen extraction software. The data were normalized by using quantile normalization (Bolstad et al., 2003)available through the Bioconductor projec(http://www.bioconductor.org), and gene calls were generated by using the RMA algorithm (Robust Multichip Average) (Irizarry et al., 2003). The relative fluorescent intensities of each ORF were scaled by assuming a constant mean signal intensity of 1,000 signal units for each array.
|
| |
|
| Submission date |
Feb 25, 2009 |
| Last update date |
Dec 31, 2010 |
| Contact name |
Xiaoyan Tang |
| E-mail(s) |
xtang@ksu.edu, llan@ksu.edu
|
| Phone |
785-532-2334
|
| Fax |
785-532-5692
|
| Organization name |
Kansas State University
|
| Department |
Plant Pathology
|
| Lab |
xiaoyan
|
| Street address |
4702 Throckmorton
|
| City |
manhattan |
| State/province |
KS |
| ZIP/Postal code |
66502 |
| Country |
USA |
| |
|
| Platform ID |
GPL3496 |
| Series (1) |
| GSE15032 |
The expression profiles of PSPTO_2222 and PSPTO_2222-2223 mutants in MM or KB |
|
