Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches

Peter V. Lovell, Nicole A. Huizinga, Abel Getachew, Brianna Mees, Samantha R. Friedrich, Morgan Wirthlin, Claudio Mello

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Objectives: Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of cDNA collections with expressed sequence tags (ESTs) and microarrays has allowed for extensive molecular characterizations of circuitry underlying vocal learning and production. However, poor database curation can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate ~ 35% of the oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches. Data description: We found that: (1) 5475 out of 43,084 oligos (a) failed to align to the zebra finch genome, (b) aligned to multiple loci, or (c) aligned to Chr-un only, and thus need to be flagged until a better genome assembly is available, or (d) reflect cloning artifacts; (2) Out of 9635 valid oligos examined further, 3120 were incorrectly named, including 1533 with no known orthologs; and (3) 2635 oligos required name update. The resulting curated dataset provides a reference for correcting gene identification errors in previous finch microarrays studies, and avoiding such errors in future studies.

Original languageEnglish (US)
Article number309
JournalBMC Research Notes
Volume11
Issue number1
DOIs
StatePublished - May 18 2018

Fingerprint

Finches
Equidae
Expressed Sequence Tags
Microarrays
Oligonucleotide Array Sequence Analysis
Gene expression
Oligonucleotides
Complementary DNA
Genes
Gene Expression
Data description
Cloning
Learning
Genome
Bioinformatics
Synteny
Gene Expression Profiling
Computational Biology
Artifacts
Names

Keywords

  • Birdsong
  • Brain
  • cDNA microarray
  • Gene expression
  • Molecular
  • Oligo array
  • Speech and language
  • Vocal learning

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches. / Lovell, Peter V.; Huizinga, Nicole A.; Getachew, Abel; Mees, Brianna; Friedrich, Samantha R.; Wirthlin, Morgan; Mello, Claudio.

In: BMC Research Notes, Vol. 11, No. 1, 309, 18.05.2018.

Research output: Contribution to journalArticle

Lovell, Peter V. ; Huizinga, Nicole A. ; Getachew, Abel ; Mees, Brianna ; Friedrich, Samantha R. ; Wirthlin, Morgan ; Mello, Claudio. / Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches. In: BMC Research Notes. 2018 ; Vol. 11, No. 1.
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