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RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers

, , , , , , , , , , , ,
1 Dermatology Research Center, School of Medicine, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia
2 Garvan Institute of Medical Research, Sydney, New South Wales, Australia
3 St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
4 Wellman Centre for Photomedicine, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United Stated of America
5 Diamantina Institute, University of Queensland, Brisbane, Outside U.S./Canada, Australia
6 Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia
DOI
10.7287/peerj.preprints.2331v1
Published
Accepted
Subject Areas
Genomics, Molecular Biology, Dermatology, Oncology, Medical Genetics
Keywords
RNA-seq, reference gene, qPCR, non-melanoma skin cancer
Copyright
© 2016 Hoang et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Hoang VL, Tom LN, Quek X, Tan J, Payne EJ, Lin LL, Sinnya S, Raphael AP, Lambie D, Frazer IH, Dinger ME, Soyer HP, Prow TW. 2016. RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers. PeerJ Preprints 4:e2331v1

Abstract

Identification of appropriate reference genes (RGs) is critical to accurate data interpretation in quantitative real-time PCR (qPCR) experiments. In this study, we have utilised next generation RNA-sequencing (RNA-seq) to analyse the transcriptome of a panel of non-melanoma skin cancer lesions, identifying genes, which are consistently expressed across all samples. Genes encoding ribosomal proteins were amongst the most stable in this dataset. Validation of this RNA-seq data was examined using qPCR to confirm the suitability of a set of highly stable genes for use as RGs. These genes will provide a valuable resource for the normalisation of qPCR data for the analysis of non-melanoma skin cancer.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Top 100 most stable genes across the dataset

DOI: 10.7287/peerj.preprints.2331v1/supp-2

Statistic of MFC, CoV and Expression Valu

DOI: 10.7287/peerj.preprints.2331v1/supp-3

Additional Information

Competing Interests

H Peter Soyer and Tarl W Prow are currently Academic Editors for PeerJ.

Author Contributions

Van LT Hoang conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Lisa N Tom conceived and designed the experiments, performed the experiments, wrote the paper, reviewed drafts of the paper.

Xiu-Cheng Quek conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.

Jean-Marie Tan performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Elizabeth J Payne performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Lynlee L Lin performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Sudipta Sinnya performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Anthony P Raphael wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Duncan Lambie performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Ian H Frazer conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Marcel E Dinger conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

H. Peter Soyer conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Tarl W Prow conceived and designed the experiments, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The study was approved by Metro South Human Research Ethics Committee and The University of Queensland Human Research Ethics Committee (HREC-11-QPAH-236, HREC-11-QPAH-477, HREC-12-QPAH-217, and HREC-12-QPAH-25)

Data Deposition

The following information was supplied regarding data availability:

Part of the raw data is included as supplementary. The raw data for the RNA-seq can be accessed via Assoc Prof Marcel Dinger's lab website http://skinref-dev.dingerlab.org/ which is also referred to within the manuscript.

Funding

This project was supported by Epiderm (Boronia Park, NSW 2111, Australia) and NHMRC Fellowships APP1109749 and APP1088318. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers
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