|
| Status |
Public on Jul 15, 2020 |
| Title |
OPSCC 7 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood serum exosomes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood serum exosomes
patient diagnosis: locally advanced oropharyngeal squamous cell carcinoma
|
| Treatment protocol |
Peripheral blood was collected into serum clot activator tubes
|
| Growth protocol |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Exosomes were isolated from the serum samples using ExoquickTm (System Biosciences, EXOQ20A-1). Extraction of miRNA from exosomes was performed using a miRNeasy Serum/Plasma kit (Qiagen, #217184) with a final elution volume of 24 microlitres ultra pure water
|
| Label |
FAM
|
| Label protocol |
PCR assays were performed by following the protocol for TaqMan@OpenArray Human MicroRNA Panel (4461104, Life technologies). For each sample, 3μl of RNA was reverse transcribed using pre-defined RT-primers (MegaplexTM Primer Human Pool A and Pool B) and the TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). Pre-amplifications were carried out with MegaplexTM PreAmp Pools and TaqMan PreAmp Master Mix on 7.5μl cDNA/ sample for each pool. The pre-amplified products (4μl per sample) were diluted at the recommended 1:40 dilution with 156μl of RNase-free ultra pure water before loading onto the 384-well TaqMan OpenArray loading plate.
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 7 -- ENT 188.1
|
| Data processing |
Expression data were processed using Quant Studio Flex software qPCR Analysis Software (Applied Biosystems™, version 1.2.2). Fluorescence data was exported to CSV files by the software for use in R statistical software.
Data were analysed in R version 3.4.2. The relative expression of each miRNA was calculated as 2(40-Ct). All possible permutations of miRNA ratios were generated from the relative expression values using R version 3.4.2.
Nested cross validation and Lasso regression were used to select a panel of micrRNA ratios to build a logisitc regression model that could differentiate healthy controls and GORDs from OPSCCs.
Matrix normalized worksheet reports the miRNA ratio expression values generated by R version 3.0.2
Fold Change worksheet reports the fold difference of expression of the microRNA ratios between the indicated study groups
|
| |
|
| Submission date |
Sep 09, 2019 |
| Last update date |
Jul 15, 2020 |
| Contact name |
Damian James Hussey |
| E-mail(s) |
damian.hussey@flinders.edu.au
|
| Organization name |
Flinders University
|
| Street address |
Flinders Drive
|
| City |
Bedford Park |
| ZIP/Postal code |
5042 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17837 |
| Series (1) |
| GSE137109 |
Cross validated serum exosomal microRNAs for the detection of oropharyngeal squamous cell carcinoma |
|
