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Series GSE63111 Query DataSets for GSE63111
Status Public on Jun 12, 2017
Title Gene expression and alternative splicing in pancreatic ductal adenocarcinoma (PDAC) [exon level]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Alternative splicing is a key event to human transcriptome and proteome diversity and complexity. Recent evidence suggests that pancreatic cancer might possess particular patterns of splice variation that influence the function of individual genes contributing to tumour progression in this disease. The identification of new pancreatic cancer-associated splice variants would offer opportunities for novel diagnostics and potentially also represent novel therapeutic targets.
In this dataset, we investigated the alterations in the splicing machinery in pancreatic adenocarcinoma (PDAC) specimens with full clinicopathological details, in comparisons to adjacent pancreatic tissues and normal tissues from donors.
Overall design We extracted total RNA from 28 PDAC specimens, 4 adjacent tissues and 2 normal pancreatic tissues from donors, and hybridized them to Affymetrix exon arrays. Affymetrix GeneChip® Human Exon 1.0 ST Arrays (Affymetrix, Santa Clara, CA, USA) were used for gene expression and alternative splicing analysis. Labelling and hybridization were performed according to the manufacturer's instructions. After scanning, .CEL files were checked for quality and analysed following the pipeline based on aroma.affymetrix R package, to produce transcript, probeset and probe-level intensities. This was followed by intensity filtering as recommended by Affymetrix.

This submission includes the exon-level analysis.
Contributor(s) Wang J, Chelala C, Crnogorac-Jurcevic T, Scapra A, Lemoine N
Citation(s) 28592875
Submission date Nov 07, 2014
Last update date Jun 12, 2017
Contact name Jun Wang
Organization name Barts Cancer Institute, Queen Mary, London
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
Platforms (1)
GPL5188 [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]
Samples (35)
GSM1363960 Donor 1, rep1 (exon level)
GSM1363961 Donor 2 (exon level)
GSM1363962 Donor 1, rep2 (exon level)
This SubSeries is part of SuperSeries:
GSE63158 Gene expression and alternative splicing in pancreatic ductal adenocarcinoma (PDAC)
BioProject PRJNA266652

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE63111_RAW.tar 785.0 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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