|
| Status |
Public on Nov 10, 2016 |
| Title |
FH09 GS |
| Sample type |
RNA |
| |
|
| Source name |
Intact Jejunum
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: intact jejunum
phenotype: gluten-sensitive
|
| Treatment protocol |
4 gluten sensitive rhesus macaques were fed gluten containing chow and 5 were normal healthy controls
|
| 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 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 |
GS
|
| Data processing |
QuantStudio™ run files from GS (n=4) and control macaques (n=5) were analyzed simultaneously using ExpressionSuite software v1.0.3 (Thermo-Fisher). Since Expression Suite software is not equipped to perform non-parametric analysis, the output file containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file, imported and analyzed by non-parametric Wilcoxon’s rank sum test for independent samples using RealTime STATMINER™ package (Integromics on Spotfire DecisionSite) designed to compare samples using the DDCT method for relative quantification of gene expression.
miRNA expression data was analyzed by normalizing to two endogenous controls (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.
RealTime STATMINER software calculates all deltadeltaCT based fold-change calculations and provides p values using the wilcoxon's rank sum test.
fold-change.txt reports test/control (i.e., GS vs Control) ratios.
|
| |
|
| Submission date |
Oct 25, 2016 |
| Last update date |
Nov 10, 2016 |
| 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) |
| GSE89170 |
Dietary Gluten-Induced Gut Dysbiosis is Accompanied by Selective Upregulation of microRNAs with Intestinal Tight Junction and Bacteria-Binding Motifs in Rhesus Macaque Model of Celiac Disease |
|
