|
| Status |
Public on Jan 11, 2010 |
| Title |
alb193_treated_male (Illumina Mouse WG-6 v2.0) |
| Sample type |
RNA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
gender: Male
age: 140 days
mutation: B6.alb/cre,Pdss2loxP/loxP
treatment: Probucol (1% wt/vol)
treatment start age: 44 days
tissue: liver
|
| Treatment protocol |
Two B6.alb/cre,Pdss2loxP/loxP mice (one male and one female) were fed standard mouse chow supplemented with probucol (1% wt/vol) from weaning beginning on day of life 44. Untreated controls consisted of two B6.alb/cre,Pdss2loxP/loxP mice (one male and one female) fed standard mouse chow.
|
| Growth protocol |
Liver-conditional knockout mice for Pdss2, a coenzyme Q biosynthetic pathway gene, were generated as previously described [9]. Briefly, the mutation was targeted to hepatocytes by utilizing mice homozygous for the floxed gene (B6.Pdss2loxP/loxP) crossed with partners that expressed cre under the control of an albumin/cre promoter (B6.Cg-Tg(alb-cre)21 Mgn/J (alb/cre)) obtained from The Jackson Lab. Animals were sacrificed and liver specimens flash frozen for RNA extraction at 140 to 169 days old. All procedures were approved by the Institutional Animal Care and Use Committee of both the University of Pennsylvania and The Children’s Hospital of Philadelphia.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each mouse was isolated by standard Trizol extraction, purified, and combined into a single aliquot from 100 mg flash-frozen liver specimens collected at the time of sacrifice, as previously described for GSE10904.
|
| Label |
Biotin-labeled target, secondary labeling using streptavidin-conjugated Cy3.
|
| Label protocol |
100 ng of total RNA was converted to cdBA and labeled using the Ambion Illumina TotalPrep Amplification Kit.
|
| |
|
| Hybridization protocol |
1.5 ug of amplified cRNA was hybridized to each section of the array at 58 degrees Centigrade for 16 hours with rocking according to the Illumina Whole Genome protocol using the IntelliHyb hybriidzation chamber.
|
| Scan protocol |
Arrays were scanned using the Illumina BeadStation 500GX scanner with high-resolution upgrade
|
| Description |
n/a
|
| Data processing |
All probes were remapped to current version of mouse coding sequence and regrouped into probe sets corresponding to NCBI genes, using AffyProbeMiner web tool. Resultant library CDF files were imported into R to process the BeadStudio-exported data with RMA method implemented in the affy package.
|
| |
|
| Submission date |
Nov 03, 2009 |
| Last update date |
Jan 11, 2010 |
| Contact name |
Marni J Falk |
| E-mail(s) |
falkm@email.chop.edu
|
| Phone |
215-590-4564
|
| Organization name |
CHOP
|
| Department |
Pediatrics/ Human Genetics
|
| Lab |
ARC 1002c
|
| Street address |
3615 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL9526 |
| Series (1) |
| GSE18677 |
Cross-platform expression microarray performance in a mouse model of mitochondrial disease therapy |
|
