|
| Status |
Public on Jun 20, 2021 |
| Title |
20140918MMi_98 I MC 113 02_02 |
| Sample type |
RNA |
| |
|
| Source name |
Tumor-free 2nd Biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
patient.id: 45
tissue: Liver tissue
fibrosis stage: F4
age: 68
liver disease: Alcohol: TRUE
liver disease: HCV: TRUE
liver disease: HBV: FALSE
liver disease: PBC: FALSE
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On average 5 sections at 10um thickness were cut from a paraffin block. Afterwards, total RNA extraction was performed using Qiagen FFPE total RNA/DNA extraction kit (Cat No./ID: 80234).
|
| Label |
nCounter
|
| Label protocol |
100 ng total RNA was prepared for miRNA expression analysis according to the nCounter® miRNA Expression Assay User Manual
|
| |
|
| Hybridization protocol |
The samples were hybridized with a panel of miRNA:tag-specific nCounter capture and barcoded reporter probes. Sample preparation was done according to the nCounter® miRNA Expression Assay User Manual. After the hybridization protocol the samples were processed on the Prep Station from NanoString.
|
| Scan protocol |
Scan protocol was performed according to the nCounter® miRNA Expression Assay User Manual. 12 samples per plate/cartridge were processed and scanned. From each patient the 1st and 2nd biopsy was always run on the same plate. Scanning was done using the Digital Analyzer.
|
| Data processing |
The raw data was normalized as described in the manual using Nsolver Software 3.0 by using the geometric mean of the top 50 most expressed miRNAs as described in the user manual and described before (e.g. Valeri N Cancer Cell 2016). Because additional samples of a related project were run at the same time on the some arrays, these additional samples were included in the normalization process, however not analyzed for the present study. These samples are labelled as "Used for normalization" in the raw data section. Samples, which did not fulfill quality criteria as described in the user manual, were excluded from further analysis. No background subtraction was performed with the NSolver Software 3.0. Data analysis was performed using the Qlucore software (Lund, Sweden). For analysis a threshold of 64 was set and all values were log transformed. Data was always analyzed paired between 1st and 2nd biopsy of the same patient (which were always run on the same plate/cartridge) using patient identification as an eliminating factor to remove batch effects between runs. Statistically significant difference between 1st and 2nd biopsy was calculated using a paired t-test.
|
| |
|
| Submission date |
Jun 20, 2018 |
| Last update date |
Jun 20, 2021 |
| Contact name |
Matthias Sebastian Matter |
| E-mail(s) |
matthias.matter@usb.ch
|
| Phone |
+41613286471
|
| Organization name |
University of Basel
|
| Department |
Institute of Pathology
|
| Street address |
Schönbeinstrasse 40
|
| City |
Basel |
| State/province |
BS |
| ZIP/Postal code |
4031 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17904 |
| Series (2) |
| GSE116043 |
miR-579-3p controls hepatocellular carcinoma formation by regulating the PI3K-AKT pathway in chronically inflamed liver (miRNA expression) |
| GSE116045 |
miR-579-3p controls hepatocellular carcinoma formation by regulating the PI3K-AKT pathway in chronically inflamed liver |
|
