|
| Status |
Public on Jun 27, 2013 |
| Title |
Detroit_control_biological_repl_3 |
| Sample type |
RNA |
| |
|
| Source name |
Detroit 562 cells uninfected
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: 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 plates (6 wells) were washed twice with PBS, after which bacteria were added at a multiplicity of infection of 10:1 (bacteria:cells). Uninfected control cells were incubated with DMEM with GlutaMAX™-I medium with 1% FCS only.
|
| 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) and DNA was removed by DNase digestion with the DNA-free kit (Ambion).
|
| Label |
5'Cy3-labeled random nonamers
|
| Label protocol |
Total RNA (5 µg) was labeled according to standard Nimblegen gene expression array protocols.
|
| |
|
| Hybridization protocol |
2 µg of labeled cDNA was applied to 12x135K pre-designed NimbleGen huamn expression arrays. Overnight hybridization at 42°C and subsequent washing of arrays was performed according to the manufacturer’s instructions (available from www.nimblegen.com).
|
| Scan protocol |
Array images were acquired with a NimbleGen MS200 scanner following their standard operation protocol, using the autogain function per subarray.
|
| Description |
Detroit-none-3
|
| Data processing |
Raw data was normalized using Arraystar (DNASTAR) software with Quantile RMA normalization.
The 'normalized_data.txt' containining RMA-normalized, averaged gene-level signal intensity (log2-transformed) is available on Series records.
|
| |
|
| Submission date |
Jun 06, 2013 |
| Last update date |
Jun 27, 2013 |
| Contact name |
Hester Bootsma |
| E-mail(s) |
h.bootsma@cukz.umcn.nl
|
| 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 |
GPL16025 |
| Series (1) |
| GSE47711 |
Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells: Expression response of human phanryngeal epithelial Detroit 562 cells to adherent Moraxella catarrhalis strain BBH18 |
|
