|
| Status |
Public on Dec 30, 2022 |
| Title |
CTR 46 |
| Sample type |
RNA |
| |
|
| Source name |
Plasma extracellular vesicles
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Plasma extracellular vesicles
disease state: healthy control
molecule subtype: microRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extracellular vesicles (EV) isolation and RNA extraction from plasma and synovial fluid was performed with the exoRNeasy Serum/Plasma Midi kit (Qiagen Italia, Milano, Italy).
|
| Label |
Applied Biosystems Human TaqMan Low Density Array (TLDA, v2.0) (Card A)
|
| Label protocol |
EV-miR were analyzed by the TaqMan Array Card Technology. EV-miR were reverse transcribed with the TaqMan microRNA Reverse Transcription Kit, using the Megaplex RT primers Human Pool A (Thermo Fisher Scientific, Monza, MB, Italy). Pre-amplification of cDNA was performed with TaqMan PreAmp Master Mix and MegaplexTM Pre-Amp primers Human Pool A. The pre-amplification product was diluted according to the manufacturer’s instructions and used to perform microRNA profiling on the ViiA 7 Real-Time PCR System.
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
Healthy controls
|
| Data processing |
Data processing, categorization, normalization, filtering, imputation and differential expression was carried out by PIPE-T galaxy tool. Ct values falling within the range 14-32 were categorized as reliable values as recommended by the manufacturer guidelines. Global mean normalization was used to reduce any technical variability introduced in the data by the RT-qPCR experiments. Only Exo-miR with at most 20% of missing values were retained for the analysis to reduce the bias introduced by imputation. Mestdagh method was employed to assign a numeric expression value to missing values. The fold change and t test method was used to identify significant differentially expressed microRNA.
non-normalized data file reports raw Ct values. Ct value of 40 indicates a missing value. Normalized data file reports delta Ct values (Ct – sample mean expression ). NA value indicates a missing value.
|
| |
|
| Submission date |
Dec 20, 2021 |
| Last update date |
Dec 30, 2022 |
| Contact name |
Federica Raggi |
| E-mail(s) |
federicaraggi@gaslini.org
|
| Organization name |
IRCCS Istituto Giannina Gaslini
|
| Lab |
Molecular biology
|
| Street address |
via genrolamo gaslini, 5
|
| City |
Genova |
| ZIP/Postal code |
16147 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19079 |
| Series (1) |
| GSE191326 |
Extracellular vesicle microRNA profiling in synovial fluids and plasma from Oligoarticular Juvenile Idiopathic Arthritis patients: methodological challenges and identification of putative disease biomarkers |
|
