|
| Status |
Public on Mar 10, 2010 |
| Title |
liver-11weeks-BxA-36 |
| Sample type |
RNA |
| |
|
| Source name |
11 weeks, liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
age: 11 weeks
other: F2 progeny produced by a B6 x A/J cross
tg (triglycerides) level: 107 micrograms/deciliter
hdl (high-density lipoproteins) level: 85 micrograms/deciliter
bodyweight: 33.69 grams
|
| Growth protocol |
Mice were sacrificed at 11 weeks of age. Livers were immediately collected and flash-frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was carried out using TRIzol reagent following the manufacturer's guidelines (Invitrogen, Carlsbad, California, USA). Samples were homogenized, using a Polytron homogenizer for one minute. RNA quality was assessed using a 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA). Following reverse transcription with an oligo(dT)-T7 primer (Affymetrix, Santa Clara, CA), double-stranded cDNA was synthesized with the superscript double-stranded cDNA synthesis custom kit (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
In an in vitro transcription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified and labeled with biotinylated nucleotides (Enzo Diagnostics, Farmingdale, NY).
|
| |
|
| Hybridization protocol |
Fifteen micrograms of biotin-labeled and fragmented cRNA was then hybridized onto Mouse Genome 430 2.0 GeneChip arrays (Affymetrix) for 16 hours at 45C. Post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
|
| Scan protocol |
Arrays were scanned with a GeneChip Scanner 3000 laser confocal slide scanner.
|
| Description |
gene expression data from the F2 progeny produced by a B6 x A/J cross
|
| Data processing |
Data was normalized with FARMS using a custom CDF mm430mmentrezgcdf.
The experimental variable measurements TG (triglycerides), HDL (high-density lipoproteins), and bodyweight were all log transformed prior to analysis to achieve symmetric distributions and to stabilize variance across the range of measured values.
|
| |
|
| Submission date |
Mar 13, 2009 |
| Last update date |
Mar 17, 2009 |
| Contact name |
Gary Churchill |
| E-mail(s) |
[email protected]
|
| Organization name |
The Jackson Laboratory
|
| Street address |
600 Main Street
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL8299 |
| Series (1) |
| GSE15226 |
Causal Modeling Using Network Ensemble Simulations Predicts Novel Lipid Metabolism Genes |
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