|
| Status |
Public on Jan 01, 2019 |
| Title |
HT22_Uninfected |
| Sample type |
RNA |
| |
|
| Source name |
Colon
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Colon
infection: Uninfected
treatment: Untreated
|
| Treatment protocol |
Twelve Indian rhesus macaques were infected intravenously with 100TCID50 dose of SIVmac251. Out of these, seven received vehicle and five were treated with delta-9-tetrahydrocannabinol. Four animals served as uninfected controls.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the miRNeasy mini kit from Qiagen Inc.
|
| Label |
Cy3
|
| Label protocol |
Total RNA from each sample was amplified and transcribed into fluorescent cRNA using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).
|
| |
|
| Hybridization protocol |
The labeled cRNAs were hybridized onto the Whole Rhesus Macaque Genome Oligo Microarray (4 x 44K, Agilent Technologies) in Agilent’s SureHyb Hybridization Chambers.
|
| Scan protocol |
After washing the slides, the arrays were scanned by the Agilent Scanner G2505C.
|
| Description |
HT22
Gene expression in colonic epithelium of uninfected rhesus macaque.
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 12 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Pathway analysis and GO Analysis were applied to determine the roles of these differentially expressed genes played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable gene expression profiling among samples.
|
| |
|
| Submission date |
Oct 17, 2018 |
| Last update date |
Jan 29, 2019 |
| Contact name |
Mahesh Mohan |
| E-mail(s) |
mmohan@txbiomed.org
|
| Organization name |
Southwest National Primate Research Center
|
| Department |
Host Pathogen Interaction Program
|
| Lab |
12/106
|
| Street address |
8715 West Military Road
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78227 |
| Country |
USA |
| |
|
| Platform ID |
GPL16027 |
| Series (2) |
| GSE121439 |
Cannabinoid attenuation of intestinal inflammation in chronic simian immunodeficiency virus (SIV)-infected rhesus macaques involves differential modulation of pro-inflammatory microRNA/gene expression and T-cell activation |
| GSE121441 |
Cannabinoid attenuation of intestinal inflammation in chronic SIV-infected rhesus macaques involves differential modulation of pro-inflammatory microRNA/gene expression and T-cell activation |
|
