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RNA-seq transcriptome analysis of male and female zebra finch cell lines

Research output: Contribution to journalArticle

  • Christopher N Balakrishnan
  • Ya-Chi Lin
  • Sarah E London
  • David F Clayton

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    Rights statement: Free via PMC Author's Post-print: green tick author can archive post-print (ie final draft post-refereeing)

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Original languageEnglish
Pages (from-to)363-369
Number of pages7
Issue number6
Publication statusPublished - Dec 2012


The derivation of stably cultured cell lines has been critical to the advance of molecular biology. We profiled gene expression in the first two generally available cell lines derived from the zebra finch. Using Illumina RNA-seq, we generated ~93 million reads and mapped the majority to the recently assembled zebra finch genome. Expression of most Ensembl-annotated genes was detected, but over half of the mapped reads aligned outside annotated genes. The male-derived G266 line expressed Z-linked genes at a higher level than did the female-derived ZFTMA line, indicating persistence in culture of the distinctive lack of avian sex chromosome dosage compensation. Although these cell lines were not derived from neural tissue, many neurobiologically relevant genes were expressed, although typically at lower levels than in a reference sample from auditory forebrain. These cell lines recapitulate fundamental songbird biology and will be useful for future studies of songbird gene regulation and function.

    Research areas

  • Animals, Auditory Cortex, Cell Line, Dosage Compensation, Genetic, Female, Finches, Gene Expression, Gene Expression Profiling, Genome, Male, Molecular Sequence Annotation, RNA, Messenger, Sequence Analysis, RNA, Sex Characteristics, Sex Chromosomes, Transcriptome

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