Microarray-based capture of novel expressed cell type-specific transfrags (CoNECT) to annotate tissue-specific transcription in drosophila melanogaster

X. Hong, H. Doddapaneni, J. M. Comeron, M. J. Rodesch, H. A. Halvensleben, C. Y. Nien, F. Bolei, R. Metpally, T. A. Richmond, T. J. Albert, J. R. Manak

Research output: Contribution to journalArticlepeer-review


Faithful annotation of tissue-specific transcript isoforms is important not only to understand how genes are organized and regulated but also to identify potential novel, unannotated exons of genes, which may be additional targets of mutation in disease states or while performing mutagenic screens. We have developed a microarray enrichment methodology followed by long-read, next-generation sequencing for identification of unannotated transcript isoforms expressed in two Drosophila tissues, the ovary and the testis. Even with limited sequencing, these studies have identified a large number of novel transcription units, including 59 exons and extensions, 39 exons and extensions, internal exons and exon extensions, gene fusions, and both germline-specific splicing events and promoters. Additionally, comparing our capture dataset with tiling array and traditional RNA-seq analysis, we demonstrate that our enrichment strategy is able to capture low-abundance transcripts that cannot readily be identified by the other strategies. Finally, we show that our methodology can help identify transcriptional signatures of minority cell types within the ovary that would otherwise be difficult to reveal without the CoNECT enrichment strategy. These studies introduce an efficient methodology for cataloging tissue-specific transcriptomes in which specific classes of genes or transcripts can be targeted for capture and sequence, thus reducing the significant sequencing depth normally required for accurate annotation.

Original languageEnglish
Pages (from-to)873-882
Number of pages10
JournalG3: Genes, Genomes, Genetics
Issue number8
StatePublished - Aug 2012


  • Array capture
  • Enrichment
  • Transcript isoforms
  • Transcriptome


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