|
| Status |
Public on Dec 31, 2018 |
| Title |
TB1003, PDAC Sample 2016 |
| Sample type |
RNA |
| |
|
| Source name |
PDAC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood mononuclear cells (PBMC) obtained from a normal donor
incubted with: serum from patients with PDAC metastasis
run date: 2016-07-21
|
| Treatment protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Growth protocol |
PBMCs were co-cultured with 40% patient serum in RPMI 1640 medium supplemented with 100 U/ml penicillin and 100 ug/ml streptomycin at 37 degrees in 5% CO2. Cultures were prepared in a Costar 24 well plate (Corning) using 500,000 cells in 500 ul of media per well. After 9 hours of culture, total RNA was extracted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and amplified using an Affymetrix Express cDNA synthesis kit (Affymetrix, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.
|
| |
|
| Hybridization protocol |
The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.
|
| Scan protocol |
After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
|
| Description |
TB1003_PDAC16
Gene expression data from PDAC
|
| Data processing |
Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through RandProd package in Bioconductor.
|
| |
|
| Submission date |
Dec 07, 2017 |
| Last update date |
Dec 31, 2018 |
| Contact name |
Martin Hessner |
| E-mail(s) |
mhessner@mcw.edu
|
| Organization name |
Medical College of Wisconsin
|
| Department |
Pediatrics
|
| Lab |
Max McGee National Research Center for Juvenile Diabetes
|
| Street address |
8701 Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE107818 |
A serum-induced transcriptome and serum cytokine signature obtained at diagnosis correlates with the development of early pancreatic ductal adenocarcinoma metastasis |
|
