|
Status |
Public on May 24, 2008 |
Title |
Male Hypox/Female Hypox 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: Hypophysectomy (‘Hypox’) 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.
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|
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Channel 2 |
Source name |
Frozen adult male rat liver tissue prepared using Trizol
|
Organism |
Rattus norvegicus |
Characteristics |
Strain: Fischer 344 Treatment: Hypophysectomy (‘Hypox’) 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.
|
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 Hypox liver pool and a single female Hypox liver pool is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in Hypox rat liver gene expression.
|
Data processing |
LOWESS normalized expression ratios, Rosetta Resolver pipeline
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|
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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) |
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