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

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题名:	Microarray-based capture of novel expressed cell type-specific transfrags (CoNECT) to annotate tissue-specific transcription in drosophila melanogaster
作者:	粘仲毅;Hong, X;Doddapaneni, H;Comeron, J M;Rodesch, M J;Halvensleben, H A;Nien, C Y;Bolei, F;Metpally, R;Richmond, T A;Albert, T J;Manak, J R
贡献者:	生醫理工學院生命科學系
关键词:	Animals;Databases, Genetic;Drosophila melanogaster - genetics;Drosophila melanogaster - metabolism;Drosophila Proteins - genetics;Drosophila Proteins - metabolism;Exons;Female;Male;Oligonucleotide Array Sequence Analysis;Ovary - metabolism;Promoter Regions, Genetic;Protein Isoforms - genetics;Protein Isoforms - metabolism;RNA Splicing;Testis - metabolism;Transcriptome
日期:	2012-08-01
上传时间:	2026-04-23 11:13:21 (UTC+8)
出版者:	Genetics Society of America;United States
摘要:	摘要： 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 5' exons and extensions, 3' 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. Ovary and testis isotigs over 200 bp have been deposited with the GenBank Transcriptome Shotgun Assembly Sequence Database as bioproject no.PRJNA89451 (accession nos. JV208106–JV230865). 出版者： United States 出版日期： 2012-08 識別號： ISSN: 2160-1836 識別號： EISSN: 2160-1836 識別號： DOI: 10.1534/g3.112.003194
显示于类别:	[生命科學系] 期刊論文

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