|
| Status |
Public on Jan 19, 2022 |
| Title |
G_5_GSP_7_tumor_30_M.txt |
| Sample type |
RNA |
| |
|
| Source name |
Plasma exosomes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Plasma exosomes
patient diagnosis: GSD1a
molecule subtype: microRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Exosomes isolation and RNA extraction from plasma 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 |
Exo-miR were analyzed by the TaqMan Array Card Technology. Exo-miR were reverse transcribed with the TaqMan microRNA Reverse Transcription Kit, using the MegaplexTM 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 ViiATM 7 Real-Time PCR System.
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
GSD1a
|
| 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 rank product method implemented by RankProd R package was used to identify significant differentially expressed microRNA.
non-normalized 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 |
Nov 16, 2021 |
| Last update date |
Jan 19, 2022 |
| Contact name |
Roberta Resaz |
| E-mail(s) |
robertaresaz@gaslini.org
|
| Organization name |
IRCCS Istituto Giannina Gaslini
|
| Lab |
Laboratory of Molecular Biology
|
| Street address |
via Gerolamo Gaslini 5
|
| City |
Genova |
| ZIP/Postal code |
16147 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17039 |
| Series (1) |
| GSE188956 |
EXOSOMAL microRNAs AS POTENTIAL BIOMARKERS OF HEPATIC INJURY AND KIDNEY DISEASE IN GLYCOGEN STORAGE DISEASE TYPE IA PATIENTS. |
|
