|
| Status |
Public on Jan 12, 2011 |
| Title |
MKN45 untreated rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
MKN45 cells untreated for 8h rep 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: gastric epithelial cells
cell line: MKN45
|
| Treatment protocol |
The morning of treatment, the cell culture medium was replaced with either fresh medium (untreated) or medium containing 10 μg/ml H. pylori lipopolysaccharide
|
| Growth protocol |
MKN45 cells were routinely maintained in RPMI (Gibco) supplemented with 10% foetal calf serum (Gibco), 2 mM L-glutamine (Sigma), 100 U/ml penicillin (Sigma) and 100 μg/ml streptomycin. The day before treatment, cells were seeded in 6-well plates at 1x106 cells/well.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
8h post-stimulation, cells were harvested and RNA isolated using the Nucleospin RNAII kit (Machery Nagel) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) using the Affymetrix IVT labeling kit.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA was hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 genechips. GeneChips were washed and stained in the Automated fluidics 450 station.
|
| Scan protocol |
Genechips were scanned using the GeneChip 3000 7G scanner
|
| Description |
gene expression in untreated MKN45 cells
|
| Data processing |
Scanned images, obtained using Affymetrix Software (MAS5), were normalized using robust multichip average (RMA) analysis with RMAExpress version 0.4.1.
|
| |
|
| Submission date |
Nov 04, 2010 |
| Last update date |
Jan 13, 2011 |
| Contact name |
Sinead Marian Smith |
| Organization name |
Trinity College Dublin
|
| Lab |
Trinity Centre for Health Sciences
|
| Street address |
St. James's Hospital
|
| City |
Dublin 8 |
| ZIP/Postal code |
D8 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE25147 |
Changes in gene expression in MKN45 cells in response to Helicobacter pylori lipopolysaccharide |
| GSE25155 |
Tribbles 3 - a novel regulator of TLR2-mediated signaling in response to Helicobacter pylori lipopolysaccharide |
|
