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Cloonan, N., Forrest, A. R. R., Kolle, G., Gardiner, B. B. A., Faulkner, G. J., Brown, M. K., Taylor, D. F., Steptoe, A. L., Wani, S., Bethel, G., Robertson, A. J., Perkins, A. C., Bruce, S. J., Lee, C. C., Ranade, S. S., Peckham, H. E., Manning, J. M., McKernan, K. J., & Grimmond, S. M. (2008). Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods, 5(7), 613–619.

Authors 19
  1. Nicole Cloonan (first)
  2. Alistair R R Forrest (additional)
  3. Gabriel Kolle (additional)
  4. Brooke B A Gardiner (additional)
  5. Geoffrey J Faulkner (additional)
  6. Mellissa K Brown (additional)
  7. Darrin F Taylor (additional)
  8. Anita L Steptoe (additional)
  9. Shivangi Wani (additional)
  10. Graeme Bethel (additional)
  11. Alan J Robertson (additional)
  12. Andrew C Perkins (additional)
  13. Stephen J Bruce (additional)
  14. Clarence C Lee (additional)
  15. Swati S Ranade (additional)
  16. Heather E Peckham (additional)
  17. Jonathan M Manning (additional)
  18. Kevin J McKernan (additional)
  19. Sean M Grimmond (additional)
References 32 Referenced 825
  1. Boguski, M.S. & Schuler, G.D. Establishing a human transcript map. Nat. Genet. 10, 369–371 (1995). (10.1038/ng0895-369) / Nat. Genet. by MS Boguski (1995)
  2. Lee, Y. et al. The TIGR gene indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res. 33, D71–D74 (2005). (10.1093/nar/gki064) / Nucleic Acids Res. by Y Lee (2005)
  3. Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005). (10.1126/science.1112014) / Science by P Carninci (2005)
  4. Kawai, J. et al. Functional annotation of a full-length mouse cDNA collection. Nature 409, 685–690 (2001). (10.1038/35055500) / Nature by J Kawai (2001)
  5. Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563–573 (2002). (10.1038/nature01266) / Nature by Y Okazaki (2002)
  6. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007). (10.1038/nature05874) / Nature by E Birney (2007)
  7. Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499–509 (2004). (10.1016/S0092-8674(04)00127-8) / Cell by S Cawley (2004)
  8. Engstrom, P.G. et al. Complex loci in human and mouse genomes. PLoS Genet. 2, 564–577 (2006). (10.1371/journal.pgen.0020047) / PLoS Genet. by PG Engstrom (2006)
  9. Kapranov, P. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484–1488 (2007). (10.1126/science.1138341) / Science by P Kapranov (2007)
  10. Gardina, P.J. et al. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics 7, 325 (2006). (10.1186/1471-2164-7-325) / BMC Genomics by PJ Gardina (2006)
  11. Clark, T.A., Sugnet, C.W. & Ares, M. Genome-wide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296, 907–910 (2002). (10.1126/science.1069415) / Science by TA Clark (2002)
  12. Reinartz, J. et al. Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Brief. Funct. Genomic. Proteomic. 1, 95–104 (2002). (10.1093/bfgp/1.1.95) / Brief. Funct. Genomic. Proteomic. by J Reinartz (2002)
  13. Velculescu, V.E. et al. Serial analysis of gene expression. Science 270, 484–487 (1995). (10.1126/science.270.5235.484) / Science by VE Velculescu (1995)
  14. Shiraki, T. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. USA 100, 15776–15781 (2003). (10.1073/pnas.2136655100) / Proc. Natl. Acad. Sci. USA by T Shiraki (2003)
  15. Kim, J.B. et al. Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science 316, 1481–1484 (2007). (10.1126/science.1137325) / Science by JB Kim (2007)
  16. Bruce, S.J. et al. Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-free (BMP4) culture. BMC Genomics 8, 365 (2007). (10.1186/1471-2164-8-365) / BMC Genomics by SJ Bruce (2007)
  17. Hirst, C.E. et al. Transcriptional profiling of mouse and human ES cells identifies SLAIN1, a novel stem cell gene. Dev. Biol. 293, 90–103 (2006). (10.1016/j.ydbio.2006.01.023) / Dev. Biol. by CE Hirst (2006)
  18. Faulkner, G.J. et al. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics 91, 281–288 (2008). (10.1016/j.ygeno.2007.11.003) / Genomics by GJ Faulkner (2008)
  19. Karolchik, D. et al. The UCSC genome browser database: 2008 update. Nucleic Acids Res. 36 (Suppl. 1), D773–779 (2008). / Nucleic Acids Res. by D Karolchik (2008)
  20. Thierry-Mieg, D. & Thierry-Mieg, J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 7 (Suppl. 1), S12 (2006). (10.1186/gb-2006-7-s1-s12) / Genome Biol. by D Thierry-Mieg (2006)
  21. Kiyosawa, H. et al. Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized. Genome Res. 15, 463–474 (2005). (10.1101/gr.3155905) / Genome Res. by H Kiyosawa (2005)
  22. Jeck, W.R. et al. Extending assembly of short DNA sequences to handle error. Bioinformatics 23, 2942–2944 (2007). (10.1093/bioinformatics/btm451) / Bioinformatics by WR Jeck (2007)
  23. Kent, W.J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002). (10.1101/gr.229202) / Genome Res. by WJ Kent (2002)
  24. Zhou, Q. et al. A gene regulatory network in mouse embryonic stem cells. Proc. Natl. Acad. Sci. USA 104, 16438–16443 (2007). (10.1073/pnas.0701014104) / Proc. Natl. Acad. Sci. USA by Q Zhou (2007)
  25. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008). (10.1016/j.cell.2008.03.029) / Cell by R Lister (2008)
  26. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science published online, doi:10.1126/science.1158441 (1 May 2008). (10.1126/science.1158441)
  27. Bruce, S.J. et al. In vitro differentiation of murine embryonic stem cells toward a renal lineage. Differentiation 75, 337–349 (2007). (10.1111/j.1432-0436.2006.00149.x) / Differentiation by SJ Bruce (2007)
  28. Matz, M. et al. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res. 27, 1558–1560 (1999). (10.1093/nar/27.6.1558) / Nucleic Acids Res. by M Matz (1999)
  29. Ohtake, H. et al. Determination of the capped site sequence of mRNA based on the detection of Cap-dependent nucleotide addition using an anchor ligation method. DNA Res. 11, 305–309 (2004). (10.1093/dnares/11.4.305) / DNA Res. by H Ohtake (2004)
  30. Schmidt, W.M. & Mueller, M.W. CapSelect: a highly sensitive method for 5′ CAP–dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs. Nucleic Acids Res. 27, e31 (1999). (10.1093/nar/27.21.e31) / Nucleic Acids Res. by WM Schmidt (1999)
  31. Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728–1732 (2005). (10.1126/science.1117389) / Science by J Shendure (2005)
  32. Smyth, G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, 3 (2004). (10.2202/1544-6115.1027) / Stat. Appl. Genet. Mol. Biol. by GK Smyth (2004)
Dates
Type When
Created 17 years, 3 months ago (May 30, 2008, 1:09 p.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 6:37 p.m.)
Indexed 4 hours ago (Sept. 3, 2025, 6:23 a.m.)
Issued 17 years, 3 months ago (May 30, 2008)
Published 17 years, 3 months ago (May 30, 2008)
Published Online 17 years, 3 months ago (May 30, 2008)
Published Print 17 years, 2 months ago (July 1, 2008)
Funders 0

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@article{Cloonan_2008, title={Stem cell transcriptome profiling via massive-scale mRNA sequencing}, volume={5}, ISSN={1548-7105}, url={http://dx.doi.org/10.1038/nmeth.1223}, DOI={10.1038/nmeth.1223}, number={7}, journal={Nature Methods}, publisher={Springer Science and Business Media LLC}, author={Cloonan, Nicole and Forrest, Alistair R R and Kolle, Gabriel and Gardiner, Brooke B A and Faulkner, Geoffrey J and Brown, Mellissa K and Taylor, Darrin F and Steptoe, Anita L and Wani, Shivangi and Bethel, Graeme and Robertson, Alan J and Perkins, Andrew C and Bruce, Stephen J and Lee, Clarence C and Ranade, Swati S and Peckham, Heather E and Manning, Jonathan M and McKernan, Kevin J and Grimmond, Sean M}, year={2008}, month=may, pages={613–619} }