|
| Status |
Public on Dec 07, 2009 |
| Title |
UCLA_mouse_liver_SM_4_94 |
| Sample type |
RNA |
| |
|
| Source name |
UCLA_EPD03P1_mouse_liver_SM_4_94
|
| Organism |
Mus musculus |
| Characteristics |
strain: SM
tissue: Liver
|
| Treatment protocol |
no treatment
|
| Growth protocol |
16 week old male mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Flash frozen samples were weighed and homogenized in Qiazol according to the manufacturer’s protocol. Following homogenization livers were isolated in RNeasy 96 columns (Qiagen) using the manufacturers protocol. RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
RNA was isolated from liver samples from animal that were either normolipidemic or hyperlipidemic through genetic perturbation. 92 strains of mice had three biological replicates, five strains had two biological replicates and two strains with one biological replicate each. All RNA samples were cleaned using a Biosprint96 (Qiagen, Valencia, CA) with RNA cleanup beads (Agencourt Bioscience, Beverly, MA) following manufacturer’s protocol with adaptations for use with the Biosprint. The quality of the total RNA from the those samples were monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and RNA quantity was measured with a NanoDrop (NanoDrop Technologies, Inc. Wilmington, DE) following the manufacturer's instructions. All samples were arrayed into three 96 well microtiter plates following a randomized design format that places samples from the same strain on different plates to better estimate variance across testing strains.
|
| |
|
| Hybridization protocol |
All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
|
| Scan protocol |
Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix). Two of 288 chips were excluded from the final analysis due to low QC scores.
|
| Description |
5500144038519011909742_D03
|
| Data processing |
The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.
|
| |
|
| Submission date |
Jun 24, 2009 |
| Last update date |
Dec 04, 2009 |
| Contact name |
brian bennett |
| E-mail(s) |
bbennett@mednet.ucla.edu
|
| Organization name |
UCLA-lusis lab
|
| Street address |
Gonda
|
| City |
los angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL8759 |
| Series (1) |
| GSE16780 |
Hybrid Mouse diversity Panel Liver Expression Profile |
|
