A team led by researchers at University of Iowa has 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. They have dubbed the method: Microarray-Based Capture of Novel Expressed Cell Type-Specific Transfrags (CoNECT).
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.
Even with limited sequencing, these studies have identified a large number of novel transcription units, including 5′ exons and extensions, 3′ exons and extensions, internal exons and exon extensions, gene fusions, and both germline-specific splicing events and promoters.
They have compared the capture dataset with tiling array and traditional RNA-seq analysis and demonstrate that their enrichment strategy is able to capture low-abundance transcripts that cannot readily be identified by the other strategies. Additionally, they show that the 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.
- Hong X, Doddapaneni H, Comeron JM, Rodesch MJ, Halvensleben HA, Nien CY, Bolei F, Metpally R, Richmond TA, Albert TJ, Manak JR. (2012) Microarray-Based Capture of Novel Expressed Cell Type-Specific Transfrags (CoNECT) to Annotate Tissue-Specific Transcription in Drosophila melanogaster. G3 (Bethesda) 2(8), 873-82. [article]