|
| Status |
Public on Feb 01, 2018 |
| Title |
HB31 |
| Sample type |
RNA |
| |
|
| Source name |
Colonic Epithelium
|
| Organism |
Macaca mulatta |
| Characteristics |
disease state: Chronic SIV
|
| Treatment protocol |
8 animals were infected intravenously with 100 TCID50 SIVmac251 and 4 (3 THC only and 1 vehicle only) 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 |
N/A
|
| 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 350 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 |
Chronic SIV-infected
|
| Data processing |
QuantStudio run files representing all treatment groups and timepoints were analyzed first using ExpressionSuite Software (Thermo Fisher). The output file from the ExpressionSuite software analysis containing five columns (well, sample, detector, task and CT values) was saved as a tab-delimited text file, imported and analyzed using the Omics Office StatMiner qPCR analysis software (TIBCO Spotfire, Perkin Elmer, Waltham, MA) using the non-parametric Mann-Whitney U test.
miRNA expression data was analyzed using global normalization method.
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.
Multiple comparisons correction was performed using Benjamini-Hochberg method for false discovery rate.
Omics Office StatMiner qPCR analysis software automatically calculates all deltadeltaCT based fold-change calculations and provides p values from the uploaded QuantStudio files. Comparisons between the two groups were made using non-parametric Mann-Whitney U test.
Fold Change worksheet reports test/control (i.e., Chronic-SIV vs uninfected control) ratios.
|
| |
|
| Submission date |
Oct 10, 2017 |
| Last update date |
Feb 01, 2018 |
| 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 (1) |
| GSE104767 |
miRNA profiling of Macaca mulatta colonic epithelium samples from chronic SIV infected rhesus macaques |
|
