|
| Status |
Public on May 14, 2014 |
| Title |
Liver_UAB30_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Liver tissue of rat with UAB30-supplemented diet for 7 days.
|
| Organism |
Rattus norvegicus |
| Characteristics |
gender: female
strain: Sprague-Dawley
tissue: liver
diet: UAB30-supplemented (200 ppm) Teklad mash (4%) diet for 7 days
age: 5 weeks
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Rat livers dissected at 5 weeks of age.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA were isolated by Trizol (Invitrogen, Carlsbad, CA) and purified using the RNeasy Mini Kit and RNase-free DNase Set (Qiagen, Valencia, CA) according to the manufacturers’ protocols.
|
| Label |
biotin
|
| Label protocol |
One microgram of each RNA sample was processed as prescribed by the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay. The GeneChip WT cDNA Synthesis Kit, cDNA Amplification Kit, and Terminal Labeling Kit (Affymetrix, Inc., Santa Clara, CA) were used for target preparation.
|
| |
|
| Hybridization protocol |
Hybridization cocktails containing 3–4 μg of fragmented, end-labeled cDNA were prepared and applied to GeneChip Rat Exon 1.0 ST arrays. The arrays were hybridized for 16 h. A wash and stain script (precommercial FS450_0001 script) was applied using the MES_EukGE-WS2v5_450-DEV fluidics station.
|
| Scan protocol |
Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.3 to produce Affymetrix CEL-formatted files which contain quantitative measures for probe hybridization.
|
| Data processing |
The probe-level data are contained in Affymetrix GeneChip Rat Exon 1.0 ST Array probe set CEL files. They were read into the R statistical software using the R/xps package [Stratowa, 2012 (http://www.bioconductor.org/packages/2.11/bioc/html/xps.html)].
RaEx-1_0-st-v1.r2.pgf
RaEx-1_0-st-v1.na31.rn4.transcript.csv
|
| |
|
| Submission date |
May 13, 2014 |
| Last update date |
May 14, 2014 |
| Contact name |
Peter Thomas Vedell |
| E-mail(s) |
vedellpt@gmail.com
|
| Organization name |
The Jackson Laboratory
|
| Street address |
600 Main Street
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL6194 |
| Series (1) |
| GSE57638 |
Effects on gene expression in rat liver after administration of RXR agonists: UAB30, 4-methyl-UAB30, and Targretin |
|
