|
| Status |
Public on Oct 01, 2007 |
| Title |
TIGR4delta-cps, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Detroit 562 infec. w. TIGR4delta-cps
|
| Organism |
Homo sapiens |
| Characteristics |
Pharyngeal epithelial cells
|
| Treatment protocol |
After a 2h incubation period, nonadherent bacteria were removed by three washes with PBS
|
| Growth protocol |
Monolayers of Detroit 562 cells in tissue culture dishes (60 mm) were washed twice with PBS, after which bacteria were added at a multiplicity of infection of 20:1 (bacteria:cells). Uninfected control cells were incubated with RPMI 1640 medium with 1% FCS only (mock-infected).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After washing, Detroit 562 cells were lysed directly in the tissue culture dish by addition of RLT buffer (Qiagen Benelux B.V.), collected with a rubber policeman, and transferred to a microcentrifuge tube. Subsequently, total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 ug of cRNA were hybridized for 16 hr on Affymetrix Human Genome U133 Plus 2.0 GeneChip s. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using an Affymetrix GeneChip Scanner.
|
| Description |
Gene expression data from pharyngeal epithelial cells
|
| Data processing |
The data were analyzed with GeneSpring 7.3. Normalization was performed by the standard RMA-algorithm. Subsequent ratios were calculated between median folds per condition and the median fold for the appropriate control condition
|
| |
|
| Submission date |
Jul 19, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Hester Bootsma |
| E-mail(s) |
[email protected]
|
| Phone |
+31-243666332
|
| Organization name |
Radboud University Medical Centre
|
| Department |
Pediatrics
|
| Lab |
Laboratory of Pediatric Infectious Diseases
|
| Street address |
Kapittelweg 29
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 EN |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE8527 |
Analysis of the in vitro transcriptional response of human pharyngeal epithelial cells to adherent pneumococci |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
