|
| Status |
Public on May 24, 2008 |
| Title |
Male Untreated/Female Untreated comparison/Replicate #1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Frozen adult female rat liver tissue prepared using Trizol
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain: Fischer 344
Treatment: untreated
Sex: female
Tissue: liver
Age: 12 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction
|
| Label |
Alexa 555
|
| Label protocol |
RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI). Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
Frozen adult male rat liver tissue prepared using Trizol
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain: Fischer 344
Treatment: untreated
Sex: male
Tissue: liver
Age: 12 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction
|
| Label |
Alexa 647
|
| Label protocol |
RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI). Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.
|
| Scan protocol |
Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).
|
| Description |
The RNA expression profile for a single male liver pool and a single female liver pool is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in untreated rat liver gene expression.
|
| Data processing |
LOWESS normalized expression ratios, Rosetta Resolver pipeline
|
| |
|
| Submission date |
May 21, 2008 |
| Last update date |
May 23, 2008 |
| Contact name |
David J. Waxman |
| E-mail(s) |
djw@bu.edu
|
| Organization name |
Boston University
|
| Department |
Department of Biology and Bioinformatics Program
|
| Street address |
5 Cummington Mall
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL4135 |
| Series (1) |
| GSE11529 |
Sex-specific early growth hormone response genes in rat liver (Rattus norvegicus) |
|
