Genome-wide expression profiles to compare array-based, RNAseq and NanoString technologies in patients with resected pancreatic ductal carcinoma.
Using formalin-fixed paraffin embedded (FFPE) tissues collected prospectively in patients with resected pancreatic ductal carcinoma (PDC) we generated genome-wide expression profiles to compare array-based, RNAseq and NanoString technologies. Samples included in the study were collected 17 patients. After careful selection by the pathologist of 17 malignant cells-enriched, 7 stroma-enriched, and 6 normal (normal pancreas in 4 cases and normal duodenum in 2 cases) regions, sections were macrodissected, and total RNA extracted. Two additional FFPE-frozen matched-paired PDAC from our local Biobank were included. Our study represents the most extensive work comparing three technologies to generate gene expression profiles from FFPE samples, and provides technical guidance for future biomarker studies in samples collected prospectively in the context of clinical trials.
- Type: Other
- Archiver: European Genome-Phenome Archive (EGA)
Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data
| Dataset ID | Description | Technology | Samples |
|---|---|---|---|
| EGAD00001003399 | Illumina HiSeq 4000 | 34 | |
| EGAD00010001273 | Affymetrix GeneChip® Human Transcriptome Array 2.0 | 34 | |
| EGAD00010001274 | Nanostring Cancer Immune | 30 | |
| EGAD00010001275 | Affymetrix GeneChip® Human Transcriptome Array 2.0 | 34 | |
| EGAD00010001276 | Nanostring cancer pathway | 30 |