|
| Status |
Public on Mar 08, 2017 |
| Title |
PANC1_T+VAL_3 |
| Sample type |
RNA |
| |
|
| Source name |
PANC-1, TGF + Valproate treated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Panc-1
treatment: TGFb1+NaValproate
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
EMT was induced by transforming growth factor-β1 (TGF-β1, R&D systems). Cells were first starved for 24 hours in 1% fetal calf serum medium to avoid interference of growth factors in the serum and then stimulated with TGF-β1 (5 ng/ml) or vehicle for 48 hours. For EMT inhibition in Panc-1 cells, acriflavine (2.5 µM, Sigma-Aldrich) or Valproate (Sodium Valproate 2 mM, Sigma-Aldrich) was added to the cell culture together with TGF-β1 for 48h.
|
| Growth protocol |
Panc-1 pancreatic cancer cells were obtained from ATCC (Rockville, MD, USA) and cultured in Gibco Modified Eagles Medium (Life Technologies) supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 U/ml Penicillin and 100 µg/ml Streptomycin.
|
| 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 200 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT PLUS 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 |
Internal Sample ID: JP312
|
| Data processing |
Data were normalized using RMA as implemented in the Affy package (version 1.44.0) of Bioconductor. Expression values are represented on a log2-scale.
|
| |
|
| Submission date |
Jun 06, 2016 |
| Last update date |
Mar 08, 2017 |
| 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 (2) |
| GSE82293 |
Acriflavine inhibits the epithelial-to-mesenchymal transition in vitro in liver and pancreatic cancer cells (part of study with TGF-b1 stimulation) |
| GSE82299 |
Acriflavine inhibits the epithelial-to-mesenchymal transition in vitro in liver and pancreatic cancer cells |
|
