|
| Status |
Public on Jul 02, 2015 |
| Title |
NL61-NASH61L |
| Sample type |
RNA |
| |
|
| Source name |
Liver, Histology class 3
|
| Organism |
Homo sapiens |
| Characteristics |
patientid: NL61
age: 58 year
gender: female
bmi: 40
tissue: liver
|
| Biomaterial provider |
University of Pretoria, Academic Hospitals
|
| Treatment protocol |
Samples collected during bariatric surgery
|
| Growth protocol |
Clinical sample prior bariatric surgery
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
|
| |
|
| Hybridization protocol |
A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix' PrimeView Human Gene Expression arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
|
| Scan protocol |
To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
|
| Description |
---
|
| Data processing |
Data were normalized using RMA as implemented in the Affy package (version 1.40.0) of Bioconductor. Expression values are represented on a log2-scale.
|
| |
|
| Submission date |
Jul 03, 2014 |
| Last update date |
Jul 02, 2015 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL15207 |
| Series (1) |
| GSE59045 |
Gene expression in liver of morbidly obese patients |
|
