|
| Status |
Public on Sep 09, 2020 |
| Title |
Plasma exosomes [KO986] |
| Sample type |
RNA |
| |
|
| Source name |
Plasma exosomes
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: LS-G6pc-/-
hepatocellular adenoma diagnosis: No tumor
amyloidosis diagnosis: Amyloidosis
cell type: Plasma exosomes
time: 1 day
|
| 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 |
FAM
|
| 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 Rodent Pool A (Thermo Fisher Scientific, Monza, MB, Italy). Pre-amplification of cDNA was performed with TaqMan PreAmp Master Mix and MegaplexTM Pre-Amp primers Rodent 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 |
KO986_G6_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA
|
| 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 5% 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 matrix file reports raw Ct values. Ct value of 40 indicates a missing value.
|
| |
|
| Submission date |
Sep 08, 2020 |
| Last update date |
Sep 09, 2020 |
| 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 |
GPL29118 |
| Series (1) |
| GSE157656 |
Circulating exosomal microRNA as potential biomarkers of hepatic injury and inflammation in glycogen storage disease type 1a |
|
