|
| Status |
Public on Jul 01, 2020 |
| Title |
JD95_Uninfected Controls |
| Sample type |
RNA |
| |
|
| Source name |
Uninfected Controls
|
| Organism |
Macaca mulatta |
| Characteristics |
Sex: male
treatment: none; untreated
tissue: oropharyngeal mucosa
|
| Treatment protocol |
7 animals were infected intravenously with 100 TCID50 SIVmac251 and 5 remained uninfected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (small and large) was extracted using the miRNeasy Mini kit (Qiagen). On-column DNase digestion was also performed to eliminate contaminating genomic DNA.
|
| Label |
FAM
|
| Label protocol |
microRNA profiling was performed using the TaqMan® OpenArray® Human microRNA panels (Life Tech) following the manufacturer’s instructions. Reverse transcription was first performed from 100 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to TLDA plates. TLDA plates were run on the ABI 7900 HT Fast PCR system following the manufacturer’s recommended thermal cycling conditions.
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
Control
|
| Data processing |
QuantStudio run files representing all treatment groups and timepoints were analyzed using ExpressionSuite Software (Life Tech). The results from the ExpressionSuite software analysis containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file which was later imported and analyzed using the Omics Office StatMiner qPCR analysis software, TIBCO Spotfire, (Perkin Elmer, Waltham, MA). Omics Office StatMiner Software utilizes the comparative Cτ (ΔΔCτ) method to rapidly and accurately quantify relative gene expression across many genes and samples.
miRNA expression data was normalized to a combination of snoU6, RNU44 and RNU48
In all experiments, the CT upper limit was set to 28 meaning that all miRNA detectors with a CT value greater than or equal to 28 were excluded.
Due to the small sample size and exploratory nature of the study multiple comparisons correction was not applied.
ExpressionSuite v1.0.3 software automatically calculates all deltadeltaCT based fold-change calculations and provides p values from the uploaded QuantStudio data files.
Fold Change worksheet reports test/control (i.e., VEH-untreated/SIV vs Uninfected control) ratios.
|
| |
|
| Submission date |
May 15, 2020 |
| Last update date |
Jul 01, 2020 |
| 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 |
GPL17837 |
| Series (2) |
| GSE150662 |
MicroRNA profiling of Oropharyngeal tissue from chronically SIV infected rhesus macaques |
| GSE151298 |
miRNA and transcriptome profiling of oropharyngeal tissue from chronically SIV infected rhesus macaques |
|
