|
| Status |
Public on Mar 08, 2010 |
| Title |
blood_RM_RRf6_SIVmac239_day217 |
| Sample type |
RNA |
| |
|
| Source name |
blood, SIVmac239 infected, chronic (180+ days)
|
| Organism |
Macaca mulatta |
| Characteristics |
gender: female
age at infection: 10.1
weight at infection (kg): 9.94
animal id: RRf6
siv strain: SIVmac239
tissue: blood
day after infection: 217
institution: University of Pennsylvania
infection group: C
bleed date: 3-3-08
rna purification date: 7-2-08
rna purification batch: 11
hybridization batch: 7
chamber batch: 15
acquisition date: 12-5-08
|
| Biomaterial provider |
Yerkes National Primate Research Center
|
| Treatment protocol |
5 sooty mangabeys and 4 rhesus macaques were inoculated intravenously with 1 ml of an uncloned strain of simian immunodeficiency virus, SIVsmm, derived from an experimentally infected SM at 11 days post-infection (1 ml of 29 plasma) as described (Gordon et al., J Immunol. 2007 Sep 1;179(5):3026-34.; Estes et al., J Immunol. 2008 May 15;180(10):6798-807.). 8 rhesus macaques were inoculated i.v. with 3000 TCID50 of SIVmac239. Blood was drawn into PaxGene RNA tubes prior to SIV infection and at post-infection times indicated.
|
| Growth protocol |
All animals used in this study were housed at the Yerkes National Primate Research Center (Atlanta, GA) in accordance with the regulations of the American Association of Accreditation of Laboratory Animal Care standards. This study was approved by the Institutional Animal Care and Usage Committees (IACUC) of Emory University and the University of Pennsylvania.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the PAXgene RNA Isolation Kit according to manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNAs were prepared using a modified version of the 2-cycle Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). 5 peptide-nucleic acid (PNA) blocking oligonucleotides directed against consensus sequences in the macaque and mangabey hemoglobin I and II genes were added into the initial reverse-transcription reaction.
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 micrograms of cRNA were diluted into 300 microlitres of hybridization cocktail, with 200 microlitres hybridized for 16 hr at 45 C on GeneChip Rhesus Macaque Genome Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
Animals had previous treatment with OKT8 antibody to deplete CD8+ T cells, and the antiretroviral drugs PMPA (tenofovir) and FTC (Emtricitabine), but were removed from treatment for >30 days prior to sampling.
GS-275
|
| Data processing |
Data from .CEL files were analyzed using Partek Genomics Suite with RMA normalization (quantile normalization, probeset summarization, RMA background subtraction).
|
| |
|
| Submission date |
May 18, 2009 |
| Last update date |
Mar 08, 2010 |
| Contact name |
Steven E Bosinger |
| E-mail(s) |
bosinger@mail.med.upenn.edu
|
| Phone |
215 5735368
|
| Fax |
215 5735369
|
| Organization name |
University of Pennsylvania
|
| Department |
Pathology and Laboratory Medicine
|
| Street address |
room 702 Stellar-Chance Laboratories, 422 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL3535 |
| Series (1) |
| GSE16147 |
Microarray Expression Analysis of SIV infection of Sooty Mangabeys |
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