|
| Status |
Public on Jan 02, 2019 |
| Title |
Temporal lobe epilepsy EpiB_10 Beaumont |
| Sample type |
RNA |
| |
|
| Source name |
plasma
|
| Organism |
Homo sapiens |
| Characteristics |
center: Beaumont
age: 25
gender: M
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 200 μl of plasma using the miRCURY RNA isolation kit-biofluid (Exiqon) according to the manufacturer’s protocol
|
| Label |
FAM
|
| Label protocol |
3 µl of total RNA was processed by reverse transcriptase and pre-amplification steps following the manufacturer’s protocol (Applied Biosystems). The pre-amplification reaction was mixed with TaqMan OpenArray Real-Time PCR Master mix (1:1). The mix was loaded onto the OpenArray human panel (755 human miRNAs) using the Accufill System and ran using a QuantStudio 12K Flex PCR (Life Technologies).
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
Post-seizure
Temporal lobe epilepsy
TaqMan OpenArray Human MicroRNA Panel and individual TaqMan Assays 96 well plate qPCR plates
|
| Data processing |
Filtering and statistical analysis of the OA miRNA profiling data were performed in R/Bioconductor. Data were first filtered according to cycle threshold (Ct< 25), amplification score (AmpScore >/= 1.24) and quantification cycle confidence (Cqconf >/= 0.8) provided by the ExpressionSuite software (ThermoFisher Scientific). Only miRNAs expressed in >80% of samples were included in the study. Missing data points were imputed. Next, we performed deltaCt normalization using miRNAs (miR-19b, miR-26a and miR-26b) that were identified by the geNorm method as being the most stable miRNAs. Differential expression analysis was then performed by applying a Student’s t-test to the normalized Ct values between each two conditions (C/EpiA, C/EpiB and EpiA/EpiB). The p-values were adjusted for multiple testing by controlling the false discovery rate (FDR) according to the method of Benjamini and Hochberg.
Matrix normalized worksheet reports DeltaCt normalized signal.
Fold Change worksheet reports log2FC, p.value and adj.p.value. FC was calculated as 2^-ΔΔCt, where -ΔΔCt = -[ΔCt_test -Δct_control]. Differential expression analysis was performed using the limma package (Ritchie et al., 2015). P-values were adjusted for multiple testing by controlling the false discovery rate (FDR) according to the method of Benjamini and Hochberg (Benjamini and Hochberg, 1995).
|
| |
|
| Submission date |
May 21, 2018 |
| Last update date |
Jan 02, 2019 |
| Contact name |
Catherine Mooney |
| E-mail(s) |
[email protected]
|
| Organization name |
University College Dublin
|
| Department |
School of Computer Science
|
| Street address |
Belfield
|
| City |
Dublin |
| ZIP/Postal code |
4 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL22992 |
| Series (2) |
| GSE114697 |
Dual-center, dual-platform microRNA profiling identifies plasma biomarkers of adult temporal lobe epilepsy (Beaumont) |
| GSE114701 |
Dual-center, dual-platform microRNA profiling identifies plasma biomarkers of adult temporal lobe epilepsy |
|
