|
| Status |
Public on Aug 15, 2009 |
| Title |
V_GSK4.CM.replicate2 |
| Sample type |
RNA |
| |
|
| Source name |
bTC3 insulinoma cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pancreas
cell type: beta cells
cell line: bTC3 insulinoma cell line
hdl preparation: GSK4
|
| Treatment protocol |
Control medium: RPMI (Gibco, catalog n° 61870) supplemented with 10% FCS and sodium pyruvate (1mM).
Vehicle: dialysis medium that is used during the HDL preparation.
|
| Growth protocol |
βTC3 cells were grown for 2 days in complete medium prior to being subjected to the indicated experimental conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed, lysed using RLT buffer (Qiagen; catalog n° 79216) and scraped off the dishes using a rubber policeman. Lysates were then added to a QIAshredder column (Qiagen kit for the isolation of total RNA from animal cells; catalog n° 74104) and spun at maximum speed in an Eppendorf centrifuge for 2 minutes at room temperature. The lysate was then frozen at -80°C. The QIAshredder unit is used to homogenize lysates and to reduce viscosity caused by high molecular weight cellular components and cell debris. RNA was then isolated and purified using the RNeasy column (Qiagen; catalog n° 74104). Total RNA was checked for quality on an RNA Nano labChip using the Bioanalyzer system (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
One μg of total RNA material was amplified and labeled with biotin according to Affymetrix protocols using the Enzo kit (Affymetrix; catalog n° 900182) for in vitro transcription.
|
| |
|
| Hybridization protocol |
Fragmented cRNA was then hybridized to Affymetrix MOE430_2 chips according to standard procedures. Samples were randomized in the labeling and hybridizing process.
|
| Scan protocol |
Hybridized chips were washed and then scanned on an Affymetrix GeneChip 3000 scanner according to the Affymetrix expression analysis technical manual.
|
| Description |
SS27520.CEL
|
| Data processing |
Gene expression signals were extracted from the scanned microarrays by the MAS 5.0 software provided by Affymetrix.
|
| |
|
| Submission date |
Aug 14, 2009 |
| Last update date |
Aug 14, 2009 |
| Contact name |
Joan Stuart |
| E-mail(s) |
[email protected]
|
| Organization name |
GSK
|
| Street address |
5 Moore Drive
|
| City |
RTP |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE17647 |
Involvement of 4E-BP1 in the protection induced by HDLs on pancreatic beta cells |
|
