|
| Status |
Public on Apr 27, 2012 |
| Title |
RJi_Week12postSIV_PBMCs |
| Sample type |
RNA |
| |
|
| Source name |
SIV infected, Control antibody treated Rhesus macaque PBMCs
|
| Organism |
Macaca mulatta |
| Characteristics |
disease state: week 12 post SIV infected
treatment: day 14 post Control antibody
tissue: PBMCs
|
| Treatment protocol |
Rhesus macaques were infected intravenously with 200 TCID50 of SIVmac251 strain. The SIV-negative animals used here were sacrificed due to neurological and mental problems but were checked to ensure no history of bowel problems.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Rneasy mini kit (Qiagen)
|
| Label |
Biotin
|
| Label protocol |
Biotinylated complementary RNAs (cRNAs) were synthesized in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix by in vitro transcription (IVT) reaction.
|
| |
|
| Hybridization protocol |
The biotinylated cRNAs were cleaned up, fragmented, and hybridized to the rhesus macaque expression arrays at 45°C for 16 h with constant rotation at 60 rpm. The gene chips were then washed and stained with Affymetrix fluidics stations 450.
|
| Scan protocol |
The gene chips were scanned on Affymetrix scanner 3000
|
| Data processing |
The images are processed to collect raw data with GeneChip Operating Software (GCOS) 1.4.
.CEL files were loaded in to Genespring GX10 software, data was preprocessed with RMA (Robost Multichip Analaysis) and per gene normaization was performed by setting measurements to median.Only those transcripts that were called present or marginal in at least one of the same condition were taken into account. Genes with statistically significant differences between the SIV infected, PD-1 antibody treated versus SIV infected, Control antibody treated group of Rhesus macaques were classified(One way ANOVA, p-value cutoff 0.05) with minimum of 1.5 fold change difference.
|
| |
|
| Submission date |
Nov 23, 2011 |
| Last update date |
Apr 27, 2012 |
| Contact name |
RAVI DYAVAR SHETTY |
| E-mail(s) |
rdyavar@emory.edu
|
| Phone |
404-727-9233
|
| Organization name |
emory university
|
| Department |
Microbiology and Immunology
|
| Lab |
Rama Amara
|
| Street address |
954 Gatewood RD NE
|
| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30329 |
| Country |
USA |
| |
|
| Platform ID |
GPL3535 |
| Series (1) |
| GSE33933 |
Gene expression in the blood of SIV infected Rhesus macaques following in vivo PD-1 blockade |
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