High-Resolution Analysis of the 5′-End Transcriptome Using a Next Generation DNA Sequencer Export

@article{citeulike:3843009, 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\^{a}€²\^{a}€ ” 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\^{a}€²-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\^{a}€²-deoxycytidine (5Aza). More than 20 million 25-base 5\^{a}€²-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\^{a}€ ” 1,000 fold greater than that observed from 5\^{a}€²end SAGE data generated from the analysis of 70,000 tags obtained by Sanger sequencing. The high-resolution 5\^{a}€²end gene expression profiling presented in this study will not only provide novel insight into the transcriptional machinery but should also serve as a basis for a better understanding of cell biology.}, author = {Hashimoto, Shin-ichi and Qu, Wei and Ahsan, Budrul and Ogoshi, Katsumi and Sasaki, Atsushi and Nakatani, Yoichiro and Lee, Yongjun and Ogawa, Masako and Ametani, Akio and Suzuki, Yutaka and Sugano, Sumio and Lee, Clarence C. and Nutter, Robert C. and Morishita, Shinichi and Matsushima, Kouji}, citeulike-article-id = {3843009}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0004108}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19119315}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19119315}, day = {1}, doi = {10.1371/journal.pone.0004108}, issn = {1932-6203}, journal = {PLoS ONE}, keywords = {5, 5prime, annotation, nextgensequencing, tag}, month = {January}, number = {1}, pages = {e4108+}, posted-at = {2009-01-02 19:12:12}, priority = {2}, publisher = {Public Library of Science}, title = {High-Resolution Analysis of the 5′-End Transcriptome Using a Next Generation DNA Sequencer}, url = {http://dx.doi.org/10.1371/journal.pone.0004108}, volume = {4}, year = {2009} }

TY - JOUR ID - citeulike:3843009 L3 - citeulike-article-id:3843009 N2 - 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 SAGE data generated from the analysis of 70,000 tags obtained by Sanger sequencing. The high-resolution 5′end gene expression profiling presented in this study will not only provide novel insight into the transcriptional machinery but should also serve as a basis for a better understanding of cell biology. IS - 1 JF - PLoS ONE SN - 1932-6203 TI - High-Resolution Analysis of the 5′-End Transcriptome Using a Next Generation DNA Sequencer PB - Public Library of Science VL - 4 SP - e4108 KW - 5 KW - 5prime KW - annotation KW - nextgensequencing KW - tag AU - Hashimoto, Shin-ichi AU - Qu, Wei AU - Ahsan, Budrul AU - Ogoshi, Katsumi AU - Sasaki, Atsushi AU - Nakatani, Yoichiro AU - Lee, Yongjun AU - Ogawa, Masako AU - Ametani, Akio AU - Suzuki, Yutaka AU - Sugano, Sumio AU - Lee, Clarence AU - Nutter, Robert AU - Morishita, Shinichi AU - Matsushima, Kouji PY - 2009/01/01/ UR - http://dx.doi.org/10.1371/journal.pone.0004108 ER -