|
| Status |
Public on Oct 27, 2020 |
| Title |
plasma-Male-4 [M04] |
| Sample type |
RNA |
| |
|
| Source name |
plasma, Male
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
age: 1
genotype: C489+2G>T/c.1558G>T
bal total cell count (per ml): 7500000
neutrophil elastase levels: 0
il-8 concentration pg/ml: 109.08
haemophilus spp.: Yes
escherichia spp.: No
staphyloccus spp.: No
antibiotictx: Yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Plasma was obtained from the study participants, RNA was isolated using the miRNeasy Serum/Plasma kit (Qiagen) and reverse transcribed using pre-defined Megaplex™ pool RT-primers.
|
| Label |
FAM
|
| Label protocol |
Pre-amplifications were performed and miRNA expression was quantified using TaqMan OpenArray Human miRNA Panels in the QuantStudio™ 12 K Flex Real-Time PCR system, allowing for 754 miRNAs to be quantified per sample.
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| 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 (Bioconductor package “Non-detects” and the data was normalised to the geometric mean (GM) as implemented in Bioconductor package “HTqPCR”. Differential expression analysis was then performed by applying a Student’s t-test to the normalized Ct values between the two conditions. The p-values were adjusted for multiple testing by controlling the false discovery rate (FDR) according to the method of Benjamini and Hochberg. Fold changes (FC) were calculated as FC = 2−∆Ct, where ∆Ct = CtmiRNA − GM.
the normalized.txt contains DeltaCt normalized signal.
|
| |
|
| Submission date |
Jun 03, 2019 |
| Last update date |
Oct 27, 2020 |
| 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 (1) |
| GSE132106 |
Plasma microRNA levels in male and female children with cystic fibrosis |
|
