|
| Status |
Public on Sep 06, 2011 |
| Title |
RM4_SIVnegative_ColorectalTissue |
| Sample type |
RNA |
| |
|
| Source name |
SIV negative Rhesus macaque Colorectal tissue
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: colorectal tissue
infection status: SIV negative
|
| Treatment protocol |
Rhesus macaques were infected intravenously with 200 TCID50 of SIVmac251 strain. In case of Sooty mangabeys,SIVsm is endemic in this population. None of the animals used in the study were experimentally infected. 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 |
Hybridization and post-hybridization processing were performed following the Affymetrix GeneChip Expression Analysis standard protocols (Affymetrix inc.)
|
| Scan protocol |
The gene chips were scanned on Affymetrix scanner 3000
|
| Description |
[Rhesus] Affymetrix Rhesus Macaque Genome Array
|
| Data processing |
The data from gene chips was processed 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 versus SIV negative group of Rhesus macaques and Sooty mangabeys were classified(Student T test, p-value cutoff 0.05) with minimum of 1.5 fold change difference.
|
| |
|
| Submission date |
Jun 15, 2011 |
| Last update date |
Sep 06, 2011 |
| 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) |
| GSE29980 |
Colorectal tissue gene expression in SIV negative and SIV positive Rhesus macaques and sooty mangabeys |
|
