|
| Status |
Public on Jun 04, 2008 |
| Title |
avirulent Rickettsia rickettsii Iowa rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
avirulent rep 2
|
| Organism |
Rickettsia rickettsii |
| Characteristics |
Iowa
|
| Growth protocol |
Monolayers of Vero cells in T25 tissue culture flasks were infected with R. rickettsii Iowa and R. rickettsii R strain at an MOI of 0.05 and grown for 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To harvest RNA the media was removed and 1 ml of Trizol (Invitrogen) was added to each T25 for RNA extraction. 200 µl of chloroform was added to the Trizol samples and spun at 13,000 rpm for 15 min. The aqueous phase (~750 µl) was removed and dried to ~200 µl and the RNA was purified using RNeasy 96 Kit (Qiagen) according to the manufactures instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.
|
| Description |
Gene expression data from__avirulent Rickettsia rickettsii Iowa_rep 2
|
| Data processing |
The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
|
| |
|
| Submission date |
Jun 06, 2007 |
| Last update date |
Jun 06, 2007 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
dsturdevant@niaid.nih.gov
|
| Phone |
4063639248
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
RTS
|
| Street address |
903 S 4th street
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL4692 |
| Series (1) |
| GSE8041 |
Genomic comparison of virulent Rickettsia rickettsii Sheila Smith and avirulent Rickettsia rickettsii Iowa |
|
