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Oxford University Press, Database, (2013), 2013

DOI: 10.1093/database/bat010

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Uncovering hidden duplicated content in public transcriptomics data

Journal article published in 2013 by Marta Rosikiewicz, Aurelie Comte, Anne Niknejad ORCID, Marc Robinson-Rechavi ORCID, Frederic B. Bastian
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

As part of the development of the database Bgee (a dataBase for Gene Expression Evolution), we annotate and analyse expression data from different types and different sources, notably Affymetrix data from GEO and ArrayExpress, and RNA-Seq data from SRA. During our quality control procedure, we have identified duplicated content in GEO and ArrayExpress, affecting ∼14% of our data: fully or partially duplicated experiments from independent data submissions, Affymetrix chips reused in several experiments, or reused within an experiment. We present here the procedure that we have established to filter such duplicates from Affymetrix data, and our procedure to identify future potential duplicates in RNA-Seq data.