|
| Status |
Public on Mar 01, 2010 |
| Title |
1_1_Control_1h_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
primary murine hepatocytes cultivated on collagen coated plates
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
gender: male
agent: Control
time: 1h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared from cultured hepatocytes with the Qiagen RNEasy plus Kit according to the manufactures instructions. For each sample, 2 million cells were used for RNA isolation and purification. Samples for microarray analysis were subjected to a quality control using an Agilent Bioanalyzer with the Pico RNA-Kit. Only RNA with a RIN better than 8.2 was used for labeling and subsequent hybridization.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
|
| Scan protocol |
Affymetrix GeneArray Scanner3001
|
| Description |
Gene expression data from primary mouse hepatocytes
|
| Data processing |
Mouse430V2 Affymetrix CEL data files were uploaded into Expressionist Refiner Array® version 4.5 (Genedata AG, Basel, Switzerland) for data condensation. Oligo hybridization intensities were condensed to probe set expression values using the MAS5 Affymetrix Statistical algorithm according to [60]. Condensed data were normalized using Expressionist Analyst® version 4.5 (Genedata AG, Basel, Switzerland). The mapping from probe-sets to genes was performed using the Phylosopher seqmap tool based on the NCBI mouse genome version 33. Absolute probe set expression values were scaled on the chip level by logarithmic mean normalization (for each chip, the geometric mean of all probe set values was scaled to 10000).
|
| |
|
| Submission date |
Dec 02, 2009 |
| Last update date |
Jan 22, 2010 |
| Contact name |
Irmgard Merfort |
| Organization name |
University of Freiburg - Institute of Pharmaceutical Science
|
| Department |
Department of Pharmaceutical Biology and Biotechnology
|
| Lab |
Merfort
|
| Street address |
Stefan-Meier-Str. 19
|
| City |
Freiburg |
| State/province |
BW |
| ZIP/Postal code |
79104 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE19272 |
Genome-wide comparison between IL-17 and combined TNF-alpha/ IL-17 induced genes in primary murine hepatocytes |
|
