Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs
available in PMC 2010 November 2.
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | en_US |
| Published: |
Nature Publishing Group
2012
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| Online Access: | http://hdl.handle.net/1721.1/73946 https://orcid.org/0000-0001-8567-2049 |
| _version_ | 1826188547725459456 |
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| author | Guttman, Mitchell Garber, Manuel Levin, Joshua Z. Donaghey, Julie Robinson, James Adiconis, Xian Fan, Lin Koziol, Magdalena J. Gnirke, Andreas Nusbaum, Chad Rinn, John L. Regev, Aviv Lander, Eric Steven |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Guttman, Mitchell Garber, Manuel Levin, Joshua Z. Donaghey, Julie Robinson, James Adiconis, Xian Fan, Lin Koziol, Magdalena J. Gnirke, Andreas Nusbaum, Chad Rinn, John L. Regev, Aviv Lander, Eric Steven |
| author_sort | Guttman, Mitchell |
| collection | MIT |
| description | available in PMC 2010 November 2. |
| first_indexed | 2024-09-23T08:01:24Z |
| format | Article |
| id | mit-1721.1/73946 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T08:01:24Z |
| publishDate | 2012 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/739462022-09-23T10:19:48Z Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs Guttman, Mitchell Garber, Manuel Levin, Joshua Z. Donaghey, Julie Robinson, James Adiconis, Xian Fan, Lin Koziol, Magdalena J. Gnirke, Andreas Nusbaum, Chad Rinn, John L. Regev, Aviv Lander, Eric Steven Massachusetts Institute of Technology. Department of Biology Guttman, Mitchell Lander, Eric S. Regev, Aviv available in PMC 2010 November 2. RNA-Seq provides an unbiased way to study a transcriptome, including both coding and noncoding genes. To date, most RNA-Seq studies have critically depended on existing annotations, and thus focused on expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We apply it to mouse embryonic stem cells, neuronal precursor cells, and lung fibroblasts to accurately reconstruct the full-length gene structures for the vast majority of known expressed genes. We identify substantial variation in protein-coding genes, including thousands of novel 5′-start sites, 3′-ends, and internal coding exons. We then determine the gene structures of over a thousand lincRNA and antisense loci. Our results open the way to direct experimental manipulation of thousands of non-coding RNAs, and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes. Merkin Family Foundation for Stem Cell Research Howard Hughes Medical Institute National Human Genome Research Institute (U.S.) Burroughs Wellcome Fund Broad Institute 2012-10-12T18:54:20Z 2012-10-12T18:54:20Z 2010-07 2010-03 Article http://purl.org/eprint/type/JournalArticle 1087-0156 1546-1696 http://hdl.handle.net/1721.1/73946 Guttman, Mitchell et al. “Ab Initio Reconstruction of Cell Type–specific Transcriptomes in Mouse Reveals the Conserved Multi-exonic Structure of lincRNAs.” Nature Biotechnology 28.5 (2010): 503–510. Web. https://orcid.org/0000-0001-8567-2049 en_US http://dx.doi.org/10.1038/nbt.1633 Nature Biotechnology Creative Commons Attribution-Noncommercial-Share Alike 3.0 http://creativecommons.org/licenses/by-nc-sa/3.0/ application/pdf Nature Publishing Group PMC |
| spellingShingle | Guttman, Mitchell Garber, Manuel Levin, Joshua Z. Donaghey, Julie Robinson, James Adiconis, Xian Fan, Lin Koziol, Magdalena J. Gnirke, Andreas Nusbaum, Chad Rinn, John L. Regev, Aviv Lander, Eric Steven Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs |
| title | Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs |
| title_full | Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs |
| title_fullStr | Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs |
| title_full_unstemmed | Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs |
| title_short | Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs |
| title_sort | ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincrnas |
| url | http://hdl.handle.net/1721.1/73946 https://orcid.org/0000-0001-8567-2049 |
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