High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer.

PloS One
Shin-ichi HashimotoKouji Matsushima

Abstract

Massively parallel, tag-based sequencing systems, such as the SOLiD system, hold the promise of revolutionizing the study of whole genome gene expression due to the number of data points that can be generated in a simple and cost-effective manner. We describe the development of a 5'-end transcriptome workflow for the SOLiD system and demonstrate the advantages in sensitivity and dynamic range offered by this tag-based application over traditional approaches for the study of whole genome gene expression. 5'-end transcriptome analysis was used to study whole genome gene expression within a colon cancer cell line, HT-29, treated with the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5Aza). More than 20 million 25-base 5'-end tags were obtained from untreated and 5Aza-treated cells and matched to sequences within the human genome. Seventy three percent of the mapped unique tags were associated with RefSeq cDNA sequences, corresponding to approximately 14,000 different protein-coding genes in this single cell type. The level of expression of these genes ranged from 0.02 to 4,704 transcripts per cell. The sensitivity of a single sequence run of the SOLiD platform was 100-1,000 fold greater than that observed from 5'end SAG...Continue Reading

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Citations

Sep 28, 2010·PPAR Research·Valerio CostaAlfredo Ciccodicola
Aug 11, 2010·Genome Biology·Steven Jm JonesMarco A Marra
May 3, 2011·PloS One·Valerio CostaAlfredo Ciccodicola
Oct 4, 2013·International Journal of Computational Biology and Drug Design·Chung-I LiYu Shyr
Apr 19, 2011·Briefings in Bioinformatics·Zhide Fang, Xiangqin Cui
Aug 13, 2011·Yi chuan = Hereditas·Xin ZhangXue-Jun Zhang
Mar 29, 2011·Drug Discovery Today·Peter M WoollardDavid J Dow
Jan 1, 2009·Drug Discovery Today. Therapeutic Strategies·Hyungsuk Kim, Raymond A Dionne
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Nov 18, 2009·The Journal of Pathology·Daphne W Bell
Aug 9, 2011·Genomics·Katsumi OgoshiKouji Matsushima
Jan 3, 2012·Seminars in Cell & Developmental Biology·Peter W HarrisonJudith E Mank
Jul 14, 2010·Journal of Biomedicine & Biotechnology·Valerio CostaAlfredo Ciccodicola
Sep 9, 2009·FEMS Microbiology Letters·Arnoud H M van Vliet
Jun 9, 2016·Expert Review of Molecular Diagnostics·Nilanjana GhoshKoel Chaudhury
Mar 20, 2013·The Journal of Immunology : Official Journal of the American Association of Immunologists·Shin-ichi HashimotoKouji Matsushima
Nov 24, 2011·Biomedical Instrumentation & Technology·Jason Launders
Aug 30, 2021·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Lei XuYuning Hu
May 3, 2013·Genome Research·Taro Leo SaitoShinichi Morishita

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Datasets Mentioned

BETA
SRA002659

Methods Mentioned

BETA
PCR
electrophoresis

Software Mentioned

Illumina
SOLiD
[UNK]
PMAGE system
SAGE

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