|
| Status |
Public on Aug 01, 2006 |
| Title |
DC-KB-36131 |
| Sample type |
RNA |
| |
|
| Source name |
Pseudomonas syringae pv. tomato DC3000.
|
| Organism |
Pseudomonas syringae pv. tomato str. DC3000 |
| Characteristics |
DC3000 were grown in KB (King et al., 1954) to ~0.7x109 cfu/mL and then are 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 when grown in KB (King et al., 1954) to ~0.7x109 cfu/mL.
|
| 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 MultichipnAverage) (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 |
May 15, 2006 |
| Last update date |
May 15, 2006 |
| Contact name |
Xiaoyan Tang |
| E-mail(s) |
[email protected], [email protected]
|
| 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) |
| GSE4848 |
Expression profiles of hrpRS- and hrpL- mutants |
|
