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

BMC Research Notes
Peter V LovellClaudio V Mello

Abstract

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. 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 microarra...Continue Reading

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Dec 19, 2014·Genome Biology·Peter V LovellClaudio V Mello
Apr 5, 2018·BMC Genomics·Peter V LovellClaudio V Mello

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Citations

Feb 11, 2020·The Journal of Comparative Neurology·Peter V LovellClaudio V Mello
Aug 4, 2019·BMC Genomics·Samantha R FriedrichClaudio V Mello
Nov 1, 2020·Scientific Reports·Alexander A NevueClaudio V Mello

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