|
| Status |
Public on Sep 01, 2011 |
| Title |
HIVTg_3mo_lung_replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
lung (right superior lobe) tissue RNA
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: HIV Tg rat, Hsd:HIV-1 (F344)
gender: male
tissue: lung
age: 3 months
|
| Growth protocol |
All rats were housed 2 per cage in a microisolator cage at a constant temperature (20–24°C) and humidity (30–60% relative humidity). Rats had access to chow and water ad libitum throughout the study period.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 25 mg of the the right superior lobe using an AllPrep DNA/RNA/protein kit, following manufacturer protocol
|
| Label |
biotin
|
| Label protocol |
Total RNA was then processed through reverse transcription to synthesize first-strand cDNA using GeneChip® 3’ IVT Express (Part #901228, Affymetrix, Santa Clara, CA). cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-congugated nucleotide (cRNA is also known as amplified RNA or aRNA).
|
| |
|
| Hybridization protocol |
The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the sample for hybridization onto GeneChip 3’ expression arrays (Part # 900506, Affymetrix Rat 230 2.0 Arrays).
|
| Scan protocol |
Standard Affymetrix scanning/image acquisition using Affymetrix GeneChip Scanner 3000 with GeneChip Command Console 4.0.0.16 software
|
| Data processing |
GeneSpringGX11.1 software (Agilent Technologies). The data were analyzed with MAS 5.0 using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500
|
| |
|
| Submission date |
Feb 17, 2011 |
| Last update date |
Sep 01, 2011 |
| Contact name |
Amie K Lund |
| E-mail(s) |
alund@lrri.org
|
| Phone |
505-348-9649
|
| Fax |
505-348-9480
|
| Organization name |
Lovelace Respiratory Research Institute
|
| Department |
Environmental and Cardiopulmonary Toxicology
|
| Street address |
2425 Ridgecrest Dr. SE
|
| City |
Albquerque |
| State/province |
NM |
| ZIP/Postal code |
87108 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE27393 |
Gene expression in lungs from male HIV transgenic rats |
|
