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Status |
Public on Dec 31, 2018 |
Title |
TB701, Non-PDAC Sample 2017 |
Sample type |
RNA |
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Source name |
Non-PDAC
|
Organism |
Homo sapiens |
Characteristics |
cell type: peripheral blood mononuclear cells (PBMC) obtained from a normal donor incubted with: serum from patients without PDAC progression run date: 2017-03-13
|
Treatment protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
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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.
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|
|
Hybridization protocol |
The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.
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Scan protocol |
After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
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Description |
TB701_NonPDAC17 Gene expression data from Non-PDAC
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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.
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|
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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 |
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