Study

Genome-wide expression profiles to compare array-based, RNAseq and NanoString technologies in patients with resected pancreatic ductal carcinoma.

Study ID Alternative Stable ID Type
EGAS00001002501 Other

Study Description

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.

Study Datasets 5 datasets.

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
RNAseq dataset of 34 samples (6 normals, 7 stroma-enriched, 21 malignant cells-enriched) from patients with resected pancreatic ductal carcinoma.
Illumina HiSeq 4000 34
EGAD00010001273
Affymetrix GeneChip® Human Transcriptome Array 2.0
Affymetrix GeneChip® Human Transcriptome Array 2.0 34
EGAD00010001274
Expression profiling by Nanostring cancer immune
Nanostring Cancer Immune 30
EGAD00010001275
Affymetrix GeneChip® Human Transcriptome Array 2.0
Affymetrix GeneChip® Human Transcriptome Array 2.0 34
EGAD00010001276
Expression profiling by Nanostring cancer pathway
Nanostring cancer pathway 30

Who archives the data?

There are no publications available