|
| Status |
Public on Oct 01, 2015 |
| Title |
PDAC_Surgery Only_Sample 4 |
| Sample type |
RNA |
| |
|
| Source name |
PDAC_untreated
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic ductal adenocarcinoma
treatment: none
|
| Treatment protocol |
Patients undergoing pancreatic resection at William Beaumont Hospital (Royal Oak, MI) were consented prior to surgery with local IRB oversight. Samples were collected at time of surgery and stored at -80°C according to CAP (College of American Pathologist)-accredited standard operating procedures. Disease pathology of frozen samples was validated with hematoxylin and eosin stained tissue sections from adjacently collected formalin fixed paraffin embedded tissue.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was homogenized with the gentleMACS Dissociator using gentleMACS M Tubes (Miltenyi Biotec Inc., Auburn, CA) prior to total RNA isolation using the Omega Total RNA Isolation Kit (Omega Bio-Tek 400, Norcross, GA). Following the manufacturer’s protocol, total RNA was purified using spin cartridge technology, quantified (Nanodrop 8000, Thermo Scientific), and stored at -80°C. RNA integrity was determined by Bioanalyzer analysis (Agilent, Santa Clara, CA) just prior to processing for expression microarray analysis.
|
| Label |
biotin
|
| Label protocol |
Using the Ambion® WT Expression Kit (Affymetrix, Santa Clara, CA), total RNA was used to generate purified sense cDNA ready for fragmentation and labeling. Fragmentation and terminal labeling was done according to manufacturer’s protocols using the GeneChip® WT Terminal Labeling and Controls Kit.
|
| |
|
| Hybridization protocol |
Hybridization to Affymetrix Human Exon 1.0 ST Arrays as well as washing and staining (with GeneChip® Fluidics Station 450, Affymetrix) were performed following manufacturer protocols.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
|
| Description |
PDAC_Surgery Only_AX0808
Gene expression data from untreated PDAC
|
| Data processing |
The CEL files containing the raw intensity data from the Affymetrix GeneChip arrays were imported into Partek Genomics Suite and normalized using the robust multichip average with a guanine-cytosine content background correction, quantile normalization, log2-transformation, and median polish probeset summarization. Exons were then summarized to genes using the average of the probesets.
probe group file: HuEx-1_0-st-v2
|
| |
|
| Submission date |
Aug 22, 2014 |
| Last update date |
Oct 01, 2015 |
| Contact name |
Bryan Thibodeau |
| E-mail(s) |
bryan.thibodeau@beaumont.edu
|
| Phone |
248-551-0275
|
| Organization name |
Beaumont Research Institute
|
| Department |
BioBank
|
| Street address |
3811 West 13 Mile Road
|
| City |
Royal Oak |
| State/province |
MI |
| ZIP/Postal code |
48073 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE60646 |
Effect of Neoadjuvant Chemoradiation on Pancreatic Adenocarcinoma |
|
