Oligonucleotide annotations from the Agilent Songbird Oligonucleotide Array V2

Posted on 01.05.2018 - 08:37
This dataset contains a set of MS Excel tables in single .xlsx files, that document the curation of a large set of oligonucleotide (oligo) annotations from the Agilent Songbird Oligonucleotide Array V2.

Table 2 summarizes the overall effort, and provides a summary breakdown of the sets of oligos analyzed in the study. Summary data include total number of oligos examined, total that passed genomic filters and those removed for further analysis (including reasoning), along with total numbers of valid oligos either analyzed further or not.

Tables 3-13 provide a list of subsets of oligos that were curated at each step of the analysis, including subsets of oligos that were removed because they were deemed uninformative (Tables 3-6), or subjected to a name verification and/or reannotation effort (Tables 8-13). The step-by-step curation of these oligos is described in the manuscript associated with this dataset.

Oligos in various categories are identified by 'oligo IDs' given by Duke University. Those subject to name verification and/or reannotation effort also have recorded the most recent oligo consensus symbols and names applied in two studies referenced in the related paper, Chromosomal and strand information to which the oligo aligns, and related HGNC ID Gene Description and HGNC Symbol Status, where relevant.

Background
Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of EST/cDNA database collections and microarrays has allowed extensive molecular characterizations of the vocal learning and production circuitry. However, poor curation of these databases 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 a large set of oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches.

CITE THIS COLLECTION

V. Lovell, Peter; Huizinga, Nicole A.; Getachew, Abel; Mees, Brianna; Friedrich, Samantha R.; Wirthlin, Morgan; et al. (2018): Oligonucleotide annotations from the Agilent Songbird Oligonucleotide Array V2. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.4081835
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