A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

by: Marc Sultan, Marcel H Schulz, Hugues Richard, Alon Magen, Andreas Klingenhoff, Matthias Scherf, Martin Seifert, Tatjana Borodina, Aleksey Soldatov, Dmitri Parkhomchuk, Dominic Schmidt, Sean O'Keeffe, Stefan Haas, Martin Vingron, Hans Lehrach, Marie-Laure Yaspo

Science (3 July 2008), 1160342.

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alternative, b_cells, expression, gene, gene_expression, gene-expression, genome-sequencing, genome-splicings, genome-transcriptome, genome-variation, method, no-tag, rna, rnaseq, rna_seq, rna-seq, sequence, sequencing, splicing, systems-biology, tba, transcription, transcriptome

Abstract

The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. Shotgun sequencing of transcripts was used to generate randomly distributed reads. Of these, 50% mapped to unique genomic location, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to non-annotated genomic regions. Based on known transcripts, RNAseq can detect 25% more genes than microarrays. A global survey of mRNA splicing events identified 94,241 splice junctions, of which 4,096 are novel, and showed that exon skipping is the most prevalent form of alternative splicing. 10.1126/science.1160342

@article{citeulike:2961451, abstract = {The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. Shotgun sequencing of transcripts was used to generate randomly distributed reads. Of these, 50\% mapped to unique genomic location, of which 80\% corresponded to known exons. We found that 66\% of the polyadenylated transcriptome mapped to known genes and 34\% to non-annotated genomic regions. Based on known transcripts, RNAseq can detect 25\% more genes than microarrays. A global survey of mRNA splicing events identified 94,241 splice junctions, of which 4,096 are novel, and showed that exon skipping is the most prevalent form of alternative splicing. 10.1126/science.1160342}, author = {Sultan, Marc and Schulz, Marcel H. and Richard, Hugues and Magen, Alon and Klingenhoff, Andreas and Scherf, Matthias and Seifert, Martin and Borodina, Tatjana and Soldatov, Aleksey and Parkhomchuk, Dmitri and Schmidt, Dominic and O'Keeffe, Sean and Haas, Stefan and Vingron, Martin and Lehrach, Hans and Yaspo, Marie-Laure }, citeulike-article-id = {2961451}, doi = {http://dx.doi.org/10.1126/science.1160342}, journal = {Science}, keywords = {gene-expression, genome-sequencing, genome-splicings, genome-transcriptome, genome-variation, systems-biology}, month = {July}, pages = {1160342+}, posted-at = {2008-07-12 05:49:09}, priority = {2}, title = {A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome}, url = {http://dx.doi.org/10.1126/science.1160342}, year = {2008} }

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TY - JOUR ID - citeulike:2961451 L3 - citeulike-article-id:2961451 TI - A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome JF - Science SP - 1160342 N2 - The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. Shotgun sequencing of transcripts was used to generate randomly distributed reads. Of these, 50% mapped to unique genomic location, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to non-annotated genomic regions. Based on known transcripts, RNAseq can detect 25% more genes than microarrays. A global survey of mRNA splicing events identified 94,241 splice junctions, of which 4,096 are novel, and showed that exon skipping is the most prevalent form of alternative splicing. 10.1126/science.1160342 KW - gene-expression KW - genome-sequencing KW - genome-splicings KW - genome-transcriptome KW - genome-variation KW - systems-biology AU - Sultan, Marc AU - Schulz, Marcel AU - Richard, Hugues AU - Magen, Alon AU - Klingenhoff, Andreas AU - Scherf, Matthias AU - Seifert, Martin AU - Borodina, Tatjana AU - Soldatov, Aleksey AU - Parkhomchuk, Dmitri AU - Schmidt, Dominic AU - O'Keeffe, Sean AU - Haas, Stefan AU - Vingron, Martin AU - Lehrach, Hans AU - Yaspo, Marie-Laure PY - 2008/07/03/ UR - http://dx.doi.org/10.1126/science.1160342 ER -

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