|
| Status |
Public on May 27, 2010 |
| Title |
FF_14 |
| Sample type |
RNA |
| |
|
| Source name |
ApoE3L.CETP mice liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: APOE*3-Leiden.CETP (E3L)
tissue: liver
agent: fenofibrate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
The Affymetrix 3’ IVT-Express labeling Kit (#901229) is used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng is used for the labeling experiments.
|
| |
|
| Hybridization protocol |
For the hybridization 15 μg cRNA is used for further fragmentation and finally 10 μg for the hybridizations. The Affymetrix Mouse Genome 430-2.0 Arrays Genome Arrays are used for hybridization. To the 270 μl hybridization cocktail, 30 μl labeled material is added according the manual of the Affymetrix 3’ IVT-Express labeling Kit.
|
| Scan protocol |
The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, staining and scanning of the chips. The Affymetrix protocols are strictly followed. The Affymetrix Command Console (v1.1) and Expression Console software (v1.1) are used to measure the performance of the washing, staining and scanning of the chips.
|
| Description |
gene expression data of ApoE3L.CETP mice liver samples treated with fenofibrate (FF)
|
| Data processing |
Raw signal intensities (from CEL files)were normalized using the GCRMA algorithm (gc-rma slow) using Management and Analysis Database for MicroArray eXperiments (MADMAX) software.
For annotation of probes and summarization of signals from probes representing one gene the MNBI custom CDF annotation file was used (based on EntrezGene, version 11.0.2 (file Matrix_customCDF - used for analysis and drawing conclusions). Genes were filtered for expression above 5 in 3 or more samples, resulting in a set of 11587 genes that was used for further analysis.
|
| |
|
| Submission date |
Apr 05, 2010 |
| Last update date |
Jul 19, 2010 |
| Contact name |
Marijana Radonjic |
| E-mail(s) |
marijana.radonjic@tno.nl
|
| Organization name |
TNO
|
| Street address |
Utrechtseweg 48
|
| City |
Zeist |
| ZIP/Postal code |
3704HE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL10288 |
| Series (1) |
| GSE21211 |
Fenofibrate increases VLDL-triglyceride production despite reducing plasma triglyceride levels in APOE*3-Leiden.CETP mice |
|
| Relations |
| Affiliated with |
GSE22940 |
