Transcriptomics

Dataset Information

3

Detecting novel low-abundant transcripts in Drosophila


ABSTRACT: Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Keywords: other

ORGANISM(S): Drosophila melanogaster  

SUBMITTER: Chung-I Wu   Wei Lin  Wei Du  Xuemei Lu  San Ming Wang  Claudia Wing  Charles Tseng  Joshua Shapiro  Deborah Johnson  Terry Clark  Yeong C Kim  Xiuqing Zhang  Huanming Yang  Jun Wang  Jingyue Bao  Min Sun  Jian Wang  Run Zhang Shi  Jinhua Xu  Guolin Zhou  Sanggyu Lee 

PROVIDER: E-GEOD-2347 | ArrayExpress | 2005-06-03

SECONDARY ACCESSION(S): GSE2347PRJNA91637

REPOSITORIES: GEO, ArrayExpress

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Publications


Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% o  ...[more]

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