메뉴 건너뛰기




Volumn 5, Issue 7, 2008, Pages 613-619

Stem cell transcriptome profiling via massive-scale mRNA sequencing

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; TRANSCRIPTOME;

EID: 46249103973     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.1223     Document Type: Article
Times cited : (846)

References (32)
  • 1
    • 0029355897 scopus 로고
    • Establishing a human transcript map
    • Boguski, M.S. & Schuler, G.D. Establishing a human transcript map. Nat. Genet. 10, 369-371 (1995).
    • (1995) Nat. Genet , vol.10 , pp. 369-371
    • Boguski, M.S.1    Schuler, G.D.2
  • 2
    • 13444273452 scopus 로고    scopus 로고
    • The TIGR gene indices: Clustering and assembling EST and known genes and integration with eukaryotic genomes
    • 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).
    • (2005) Nucleic Acids Res , vol.33
    • Lee, Y.1
  • 3
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559-1563 (2005).
    • (2005) Science , vol.309 , pp. 1559-1563
    • Carninci, P.1
  • 4
    • 0035825662 scopus 로고    scopus 로고
    • Functional annotation of a full-length mouse cDNA collection
    • Kawai, J. et al. Functional annotation of a full-length mouse cDNA collection. Nature 409, 685-690 (2001).
    • (2001) Nature , vol.409 , pp. 685-690
    • Kawai, J.1
  • 5
    • 0142104045 scopus 로고    scopus 로고
    • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    • Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420 563-573 (2002).
    • (2002) Nature , vol.420 , pp. 563-573
    • Okazaki, Y.1
  • 6
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • 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).
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1
  • 7
    • 10744226888 scopus 로고    scopus 로고
    • Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    • 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).
    • (2004) Cell , vol.116 , pp. 499-509
    • Cawley, S.1
  • 8
    • 33646473694 scopus 로고    scopus 로고
    • Complex loci in human and mouse genomes
    • Engstrom, P.G. et al. Complex loci in human and mouse genomes. PLoS Genet. 2, 564-577 (2006).
    • (2006) PLoS Genet , vol.2 , pp. 564-577
    • Engstrom, P.G.1
  • 9
    • 34250160256 scopus 로고    scopus 로고
    • RNA maps reveal new RNA classes and a possible function for pervasive transcription
    • Kapranov, P. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484-1488 (2007).
    • (2007) Science , vol.316 , pp. 1484-1488
    • Kapranov, P.1
  • 10
    • 33846467191 scopus 로고    scopus 로고
    • Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array
    • 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).
    • (2006) BMC Genomics , vol.7 , pp. 325
    • Gardina, P.J.1
  • 11
    • 0037012922 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA processing in yeast using splicing-specific microarrays
    • 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).
    • (2002) Science , vol.296 , pp. 907-910
    • Clark, T.A.1    Sugnet, C.W.2    Ares, M.3
  • 12
    • 3242875708 scopus 로고    scopus 로고
    • Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms
    • 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).
    • (2002) Brief. Funct. Genomic. Proteomic , vol.1 , pp. 95-104
    • Reinartz, J.1
  • 13
    • 0028789793 scopus 로고
    • Serial analysis of gene expression
    • Velculescu, V.E. et al. Serial analysis of gene expression. Science 270, 484-487 (1995).
    • (1995) Science , vol.270 , pp. 484-487
    • Velculescu, V.E.1
  • 14
    • 9144233601 scopus 로고    scopus 로고
    • Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
    • 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).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 15776-15781
    • Shiraki, T.1
  • 15
    • 34250201129 scopus 로고    scopus 로고
    • Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy
    • Kim, J.B. et al. Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science 316, 1481-1484 (2007).
    • (2007) Science , vol.316 , pp. 1481-1484
    • Kim, J.B.1
  • 16
    • 38349126303 scopus 로고    scopus 로고
    • Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-free (BMP4) culture
    • 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).
    • (2007) BMC Genomics , vol.8 , pp. 365
    • Bruce, S.J.1
  • 17
    • 33646485820 scopus 로고    scopus 로고
    • Transcriptional profiling of mouse and human ES cells identifies SLAIN1, a novel stem cell gene
    • 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).
    • (2006) Dev. Biol , vol.293 , pp. 90-103
    • Hirst, C.E.1
  • 18
    • 39149083734 scopus 로고    scopus 로고
    • A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE
    • 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).
    • (2008) Genomics , vol.91 , pp. 281-288
    • Faulkner, G.J.1
  • 19
    • 38549131376 scopus 로고    scopus 로고
    • The UCSC genome browser database: 2008 update
    • Karolchik, D. et al. The UCSC genome browser database: 2008 update. Nucleic Acids Res. 36 (Suppl. 1), D773-779 (2008).
    • (2008) Nucleic Acids Res , vol.36 , Issue.SUPPL. 1
    • Karolchik, D.1
  • 20
    • 33748486517 scopus 로고    scopus 로고
    • AceView: A comprehensive cDNA-supported gene and transcripts annotation
    • S
    • Thierry-Mieg, D. & Thierry-Mieg, J. AceView: A comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 7 (Suppl. 1), S12 (2006).
    • (2006) Genome Biol , vol.7 , Issue.SUPPL. 1 , pp. 12
    • Thierry-Mieg, D.1    Thierry-Mieg, J.2
  • 21
    • 17844363942 scopus 로고    scopus 로고
    • Disclosing hidden transcripts: Mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized
    • 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).
    • (2005) Genome Res , vol.15 , pp. 463-474
    • Kiyosawa, H.1
  • 22
    • 36448948250 scopus 로고    scopus 로고
    • Extending assembly of short DNA sequences to handle error
    • Jeck, W.R. et al. Extending assembly of short DNA sequences to handle error. Bioinformatics 23, 2942-2944 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 2942-2944
    • Jeck, W.R.1
  • 23
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - the BLAST-like alignment tool
    • Kent, W.J. BLAT - the BLAST-like alignment tool. Genome Res. 12 656-664 (2002).
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 24
    • 36749083429 scopus 로고    scopus 로고
    • A gene regulatory network in mouse embryonic stem cells
    • Zhou, Q. et al. A gene regulatory network in mouse embryonic stem cells. Proc. Natl. Acad. Sci. USA 104, 16438-16443 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 16438-16443
    • Zhou, Q.1
  • 25
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    • Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
    • (2008) Cell , vol.133 , pp. 523-536
    • Lister, R.1
  • 26
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • doi:10.1126/science.1158441 1 May
    • 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).
    • (2008) Science published online
    • Nagalakshmi, U.1
  • 27
    • 34249087679 scopus 로고    scopus 로고
    • In vitro differentiation of murine embryonic stem cells toward a renal lineage
    • Bruce, S.J. et al. In vitro differentiation of murine embryonic stem cells toward a renal lineage. Differentiation 75, 337-349 (2007).
    • (2007) Differentiation , vol.75 , pp. 337-349
    • Bruce, S.J.1
  • 28
    • 0033559113 scopus 로고    scopus 로고
    • Amplification of cDNA ends based on template-switching effect and step-out PCR
    • Matz, M. et al. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res. 27, 1558-1560 (1999).
    • (1999) Nucleic Acids Res , vol.27 , pp. 1558-1560
    • Matz, M.1
  • 29
    • 11144326722 scopus 로고    scopus 로고
    • Determination of the capped site sequence of mRNA based on the detection of Cap-dependent nucleotide addition using an anchor ligation method
    • 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).
    • (2004) DNA Res , vol.11 , pp. 305-309
    • Ohtake, H.1
  • 30
    • 0033228157 scopus 로고    scopus 로고
    • CapSelect: A highly sensitive method for 5′ CAP-dependent enrichment of full-Length cDNA in PCR-mediated analysis of mRNAs
    • 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).
    • (1999) Nucleic Acids Res , vol.27
    • Schmidt, W.M.1    Mueller, M.W.2
  • 31
    • 24644462173 scopus 로고    scopus 로고
    • Accurate multiplex polony sequencing of an evolved bacterial genome
    • Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728-1732 (2005).
    • (2005) Science , vol.309 , pp. 1728-1732
    • Shendure, J.1
  • 32
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • Smyth, G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, 3 (2004).
    • (2004) Stat. Appl. Genet. Mol. Biol , vol.3 , pp. 3
    • Smyth, G.K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.