Oligonucleotide annotations from the Agilent Songbird Oligonucleotide Array V2: data file 3

This dataset contains a single MS Excel <b>.xlsx</b> file, documenting the curation of a large set of oligonucleotide (oligo) annotations from the Agilent Songbird Oligonucleotide Array V2.<br><b>Tables 3-13</b> 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 (<b>Tables 3-6</b>), or subjected to a name verification and/or reannotation effort (<b>Tables 8-13</b>). The step-by-step curation of these oligos is described in the manuscript associated with this dataset.<br>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.<br><b>Background</b>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.<br><br>

**本数据集包含单个Microsoft Excel（MS Excel）格式的.xlsx文件，记录了安捷伦（Agilent）Songbird寡核苷酸芯片V2中大量寡核苷酸（oligo）注释信息的整理流程。**

**表格3至13** 列出了分析各环节中经整理的寡核苷酸子集，其中包括因被判定为无信息而被剔除的寡核苷酸子集（**表格3至6**），以及经过名称验证和/或重新注释流程的寡核苷酸子集（**表格8至13**）。本数据集配套的研究手稿中详细阐述了这些寡核苷酸的分步整理流程。

不同类别的寡核苷酸均采用杜克大学（Duke University）提供的“寡核苷酸编号（oligo IDs）”进行标识。经过名称验证和/或重新注释流程的寡核苷酸，还附带了相关论文引用的两项研究中使用的最新寡核苷酸共识符号与名称、寡核苷酸比对所对应的染色体及链信息，以及相关的人类基因命名委员会（HGNC）编号、基因描述与HGNC符号状态（如适用）。

**背景**
斑胸草雀是研究发声学习机制的重要模式生物，而发声学习是支撑人类口语语言形成的关键性状。表达序列标签（EST）/互补DNA（cDNA）数据库集合以及微阵列技术的发展，使得研究人员能够对发声学习与发声产生回路开展广泛的分子表征研究。然而，这些数据库的整理质量不佳可能会导致转录组学与生物信息学分析出现误差，限制了这些资源的应用价值。本研究通过基因组比对和共线性分析开展直系同源验证，对用于斑胸草雀基因表达分析的安捷伦（Agilent）微阵列中包含的大量寡核苷酸及对应的EST/cDNA进行了整理与重新注释。