Uncovering hidden duplicated content in public transcriptomics data

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. Database URL: http://bgee.unil.ch/

• Publication year

  2013

• Venue

  Database J. Biol. Databases Curation

• Publication date

  2013-03-13

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/database/bat010PMID 23487185PMCID 3595988
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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