|
| Status |
Public on Oct 01, 2012 |
| Title |
Control liquid diet, biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Control, biological replicate 3
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Lieber-DeCarli liquid control diet
genetic background: C57BL/6
tissue: liver
gender: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted from frozen liver tissue using TRIzol reagent (Invitrogen) and purified by RNeasy MinElute Cleanup (Qiagen, GmbH).
|
| Label |
Biotin
|
| Label protocol |
500 ng RNA is converted to double-stranded cDNA, followed by an amplification step (in vitro transcription, IVT) to generate biotin labeled cRNA.
|
| |
|
| Hybridization protocol |
1.5µg cRNA were subsequently hybridized to Illumina MouseRef-8 v2.0 expression beadchip (Illumina, San Diego, CA) at 58 C. After 14-20 hours hybridization, the BeadChip were stained by Cy3 and washed.
|
| Scan protocol |
Intensities of bead fluorescence were detected by the Illumina BeadArray Reader.
|
| Data processing |
Raw intensity values were exported from GenomeStudio software for data processing and statistical computing in R (http://www.R-project.org) and Bioconductor (http://www.bioconductor.org). Microarray probes with detection p-value less than 0.05 were considered to be present in the analysis. Data quality of the probes was assessed using the Lumi - a Bioconductor package to process Illumina microarray data (Du et al., 2008). A robust spline normalization (RSN) method in the Lumi package that combines the features of the quantile and loess normalization methods was used for normalization of the data. Limma – a Bioconductor R package was used to identify differentially expressed genes among groups.
|
| |
|
| Submission date |
Aug 23, 2012 |
| Last update date |
Oct 01, 2012 |
| Contact name |
Lee-Yan Sheen |
| E-mail(s) |
lysheen@ntu.edu.tw
|
| Phone |
+886-2-33664129
|
| Fax |
+886-2-23620849
|
| URL |
http://www.fst.ntu.edu.tw/teacher/sun/r104_eng.htm
|
| Organization name |
National Taiwan University
|
| Department |
Institute of Food Science and Technology
|
| Lab |
Lab of Dietary Therapy
|
| Street address |
No. 1, Sec 4, Roosevelt Road,
|
| City |
TAIPEI |
| ZIP/Postal code |
10617 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE40334 |
Transcriptome analysis of garlic induced hepatoprotection against alcoholic fatty liver |
|
