|
| Status |
Public on Dec 10, 2010 |
| Title |
FXRSHPko.3wk.rep2 |
| Sample type |
RNA |
| |
|
| Source name |
mouse liver
|
| Organism |
Mus musculus |
| Characteristics |
age: 3 weeks
strain: C57Bl/6
gender: male
tissue: liver
genome/variation: FXR-/-,SHP-/- double knock out
|
| Growth protocol |
Individual FXR-/- or SHP-/- mice were backcrossed with C57BL/6 mice to generate congenic C57BL/6 FXR-/- or SHP-/- mice. Congenic single knockout animals were bred with each other to generate FXR/SHP double knockout mice. Age-matched, male, DKO congenic and C57BL/6 wild-type (WT) mice were used throughout this study. WT control mice (C57BL/6) were purchased from Harlan Sprague Dawley, Inc. (Indianapolis, IN). Mice were sacrificed at 3 or 5 weeks after birth. Mice were housed on a standard 12-hour light/dark cycle and were fed normal chow and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared according to manufacturer’s protocol. (Trizol, Invitrogen). The RNA obtained was further purified using qiagen columns.
|
| Label |
biotin
|
| Label protocol |
500 ng of total RNA was reverse transcribed into cRNA and biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion). cRNA was quantified using an Agilent Bioanalyzer 2100
|
| |
|
| Hybridization protocol |
Labeled cRNA was hybridized to the Illumina mouse REF8 v1.1 Expression BeadChip using standard protocols (Illumina).
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
Gene expression in 3wk old FXR-/-/SHP-/- mouse liver
|
| Data processing |
The probe profile output from the Illumina BeadStudio toolkit was read into R using the lumi BioC package. Then, the data was VST transformed (Lin, S.M., Du, P., Huber, W., and Kibbe, W.A. 2008. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res 36:e11) followed by quantile normalization. The versions of software and BioC packages were as follows: R_2.8.0, lumi_1.8.2.
|
| |
|
| Submission date |
Mar 02, 2010 |
| Last update date |
Dec 10, 2010 |
| Contact name |
Scott Andrew Ochsner |
| E-mail(s) |
sochsner@bcm.edu
|
| Phone |
713-798-6227
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Cellular Biology
|
| Lab |
SPP: Signaling Pathways Project
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL6103 |
| Series (1) |
| GSE20599 |
Gene expression analysis of FXR null, SHP null, and double FXR/SHP null mice |
|
