메뉴 건너뛰기




Volumn 4, Issue 9, 2014, Pages 1765-1772

A new dataset of spermatogenic vs. oogenic transcriptomes in the nematode Caenorhabditis elegans

Author keywords

C. elegans; Genetics of sex; Germline sex; RNA Seq; Splicing

Indexed keywords

TRANSCRIPTOME; HELMINTH RNA;

EID: 84907909060     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.114.012351     Document Type: Article
Times cited : (110)

References (48)
  • 1
    • 84904250154 scopus 로고    scopus 로고
    • Sex-biased gene expression and evolution of the X chromosome in nematodes
    • Albritton, S. E., A. L. Kranz, P. Rao, M. Kramer, C. Dieterich et al., 2014 Sex-biased gene expression and evolution of the X chromosome in nematodes. Genetics 197: 865-883.
    • (2014) Genetics , vol.197 , pp. 865-883
    • Albritton, S.E.1    Kranz, A.L.2    Rao, P.3    Kramer, M.4    Dieterich, C.5
  • 2
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S., and W. Huber, 2010 Differential expression analysis for sequence count data. Genome Biol. 11: R106.
    • (2010) Genome Biol , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 3
    • 84865527768 scopus 로고    scopus 로고
    • Detecting differential usage of exons from RNA-seq data
    • Anders, S., A. Reyes, and W. Huber, 2012 Detecting differential usage of exons from RNA-seq data. Genome Res. 22: 2008-2017.
    • (2012) Genome Res , vol.22 , pp. 2008-2017
    • Anders, S.1    Reyes, A.2    Huber, W.3
  • 4
    • 0023086986 scopus 로고
    • Gain-of-function mutations of fem-3, a sex-determination gene in Caenorhabditis elegans
    • Barton, M. K., T. B. Schedl, and J. Kimble, 1987 Gain-of-function mutations of fem-3, a sex-determination gene in Caenorhabditis elegans. Genetics 115: 107-119.
    • (1987) Genetics , vol.115 , pp. 107-119
    • Barton, M.K.1    Schedl, T.B.2    Kimble, J.3
  • 5
    • 0037350760 scopus 로고    scopus 로고
    • Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome
    • Baugh, L. R., A. A. Hill, D. K. Slonim, E. L. Brown, and C. P. Hunter, 2003 Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome. Development 130: 889-900.
    • (2003) Development , vol.130 , pp. 889-900
    • Baugh, L.R.1    Hill, A.A.2    Slonim, D.K.3    Brown, E.L.4    Hunter, C.P.5
  • 6
    • 0032509302 scopus 로고    scopus 로고
    • Genome sequence of the nematode C elegans: a platform for investigating biology.
    • C. elegans Sequencing Consortium, 1998 Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018.
    • (1998) Science , vol.282 , pp. 2012-2018
  • 7
    • 0033972414 scopus 로고    scopus 로고
    • A novel member of the Tob family of proteins controls sexual fate in Caenorhabditis elegans germ cells
    • Chen, P.-J., A. Singal, J. Kimble, and R. E. Ellis, 2000 A novel member of the Tob family of proteins controls sexual fate in Caenorhabditis elegans germ cells. Dev. Biol. 217: 77-90.
    • (2000) Dev. Biol , vol.217 , pp. 77-90
    • Chen, P.-J.1    Singal, A.2    Kimble, J.3    Ellis, R.E.4
  • 9
    • 84890860526 scopus 로고    scopus 로고
    • Argonautes promote male fertility and provide a paternal memory of germline gene expression in C elegans.
    • Conine, C. C., J. J. Moresco, W. Gu, M. Shirayama, D. Conte, Jr. et al., 2013 Argonautes promote male fertility and provide a paternal memory of germline gene expression in C. elegans. Cell 155: 1532-1544.
    • (2013) Cell , vol.155 , pp. 1532-1544
    • Conine, C.C.1    Moresco, J.J.2    Gu, W.3    Shirayama, M.4    Conte Jr., D.5
  • 10
    • 0032493878 scopus 로고    scopus 로고
    • Meiotic recombination in C elegans initiates by a conserved mechanism and is dispensable for homologous chromosome synapsis.
    • Dernburg, A. F., K. McDonald, G. Moulder, R. Barstead, M. Dresser et al., 1998 Meiotic recombination in C. elegans initiates by a conserved mechanism and is dispensable for homologous chromosome synapsis. Cell 94: 387-398.
    • (1998) Cell , vol.94 , pp. 387-398
    • Dernburg, A.F.1    McDonald, K.2    Moulder, G.3    Barstead, R.4    Dresser, M.5
  • 11
    • 0035433726 scopus 로고    scopus 로고
    • Two zinc finger proteins, OMA-1 and OMA-2, are redundantly required for oocyte maturation in C elegans.
    • Detwiler, M. R., M. Reuben, X. Li, E. Rogers, and R. Lin, 2001 Two zinc finger proteins, OMA-1 and OMA-2, are redundantly required for oocyte maturation in C. elegans. Dev. Cell 1: 187-199.
    • (2001) Dev. Cell , vol.1 , pp. 187-199
    • Detwiler, M.R.1    Reuben, M.2    Li, X.3    Rogers, E.4    Lin, R.5
  • 14
    • 0034980967 scopus 로고    scopus 로고
    • Germline and developmental roles of the nuclear transport factor importin a3 in C elegans.
    • Geles, K. G., and S. A. Adam, 2001 Germline and developmental roles of the nuclear transport factor importin a3 in C. elegans. Development 128: 1817-1830.
    • (2001) Development , vol.128 , pp. 1817-1830
    • Geles, K.G.1    Adam, S.A.2
  • 15
    • 78650410139 scopus 로고    scopus 로고
    • Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    • Gerstein, M. B., Z. J. Lu, E. L. Van Nostrand, C. Cheng, B. I. Arshinoff et al., 2010 Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330: 1775-1787.
    • (2010) Science , vol.330 , pp. 1775-1787
    • Gerstein, M.B.1    Lu, Z.J.2    Van Nostrand, E.L.3    Cheng, C.4    Arshinoff, B.I.5
  • 16
    • 0032734242 scopus 로고    scopus 로고
    • Receptor-mediated endocytosis in the Caenorhabditis elegans oocyte
    • Grant, B., and D. Hirsh, 1999 Receptor-mediated endocytosis in the Caenorhabditis elegans oocyte. Mol. Biol. Cell 10: 4311-4326.
    • (1999) Mol. Biol. Cell , vol.10 , pp. 4311-4326
    • Grant, B.1    Hirsh, D.2
  • 18
    • 0017230019 scopus 로고
    • Development of the reproductive system of Caenorhabditis elegans
    • Hirsh, D., D. Oppenheim, and M. Klass, 1976 Development of the reproductive system of Caenorhabditis elegans. Dev. Biol. 49: 200-219.
    • (1976) Dev. Biol , vol.49 , pp. 200-219
    • Hirsh, D.1    Oppenheim, D.2    Klass, M.3
  • 19
    • 34447636082 scopus 로고    scopus 로고
    • Differential timing of S phases, X chromosome replication, and meiotic prophase in the C elegans germ line.
    • Jaramillo-Lambert, A., M. Ellefson, A. M. Villeneuve, and J. Engebrecht, 2007 Differential timing of S phases, X chromosome replication, and meiotic prophase in the C. elegans germ line. Dev. Biol. 308: 206-221.
    • (2007) Dev. Biol , vol.308 , pp. 206-221
    • Jaramillo-Lambert, A.1    Ellefson, M.2    Villeneuve, A.M.3    Engebrecht, J.4
  • 20
    • 83455219453 scopus 로고    scopus 로고
    • In vivo and transcriptome-wide identification of RNA binding protein target sites
    • Jungkamp, A. C., M. Stoeckius, D. Mecenas, D. Grun, G. Mastrobuoni et al., 2011 In vivo and transcriptome-wide identification of RNA binding protein target sites. Mol. Cell 44: 828-840.
    • (2011) Mol. Cell , vol.44 , pp. 828-840
    • Jungkamp, A.C.1    Stoeckius, M.2    Mecenas, D.3    Grun, D.4    Mastrobuoni, G.5
  • 21
    • 77951536653 scopus 로고    scopus 로고
    • PRP-17 and the pre-mRNA splicing pathway are preferentially required for the proliferation vs meiotic development decision and germline sex determination in Caenorhabditis elegans.
    • Kerins, J. A., M. Hanazawa, M. Dorsett, and T. Schedl, 2010 PRP-17 and the pre-mRNA splicing pathway are preferentially required for the proliferation vs. meiotic development decision and germline sex determination in Caenorhabditis elegans. Dev. Dyn. 239: 1555-1572.
    • (2010) Dev. Dyn , vol.239 , pp. 1555-1572
    • Kerins, J.A.1    Hanazawa, M.2    Dorsett, M.3    Schedl, T.4
  • 22
    • 77649264236 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator
    • Kershner, A. M., and J. Kimble, 2010 Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator. Proc. Natl. Acad. Sci. USA 107: 3936-3941.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 3936-3941
    • Kershner, A.M.1    Kimble, J.2
  • 23
    • 65549130875 scopus 로고    scopus 로고
    • Antagonism between GLD-2 binding partners controls gamete sex
    • Kim, K. W., K. Nykamp, N. Suh, J. L. Bachorik, L. Wang et al., 2009 Antagonism between GLD-2 binding partners controls gamete sex. Dev. Cell 16: 723-733.
    • (2009) Dev. Cell , vol.16 , pp. 723-733
    • Kim, K.W.1    Nykamp, K.2    Suh, N.3    Bachorik, J.L.4    Wang, L.5
  • 24
    • 78049253481 scopus 로고    scopus 로고
    • GLD-2/RNP-8 cytoplasmic poly(A) polymerase is a broad-spectrum regulator of the oogenesis program
    • Kim, K. W., T. L. Wilson, and J. Kimble, 2010 GLD-2/RNP-8 cytoplasmic poly(A) polymerase is a broad-spectrum regulator of the oogenesis program. Proc. Natl. Acad. Sci. USA 107: 17445-17450.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 17445-17450
    • Kim, K.W.1    Wilson, T.L.2    Kimble, J.3
  • 25
    • 36849045088 scopus 로고    scopus 로고
    • Controls of germline stem cells, entry into meiosis, and the sperm/oocyte decision in Caenorhabditis elegans
    • Kimble, J., and S. L. Crittenden, 2007 Controls of germline stem cells, entry into meiosis, and the sperm/oocyte decision in Caenorhabditis elegans. Annu. Rev. Cell Dev. Biol. 23: 405-433.
    • (2007) Annu. Rev. Cell Dev. Biol , vol.23 , pp. 405-433
    • Kimble, J.1    Crittenden, S.L.2
  • 26
    • 84872686356 scopus 로고    scopus 로고
    • Tissuespecific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs
    • Kudron, M., W. Niu, Z. Lu, G. Wang, M. Gerstein et al., 2013 Tissuespecific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biol. 14: R5.
    • (2013) Genome Biol , vol.14 , pp. R5
    • Kudron, M.1    Niu, W.2    Lu, Z.3    Wang, G.4    Gerstein, M.5
  • 28
  • 30
    • 0034668008 scopus 로고    scopus 로고
    • CPEB proteins control two key steps in spermatogenesis in C elegans.
    • Luitjens, C., M. Gallegos, B. Kraemer, J. Kimble, and M. Wickens, 2000 CPEB proteins control two key steps in spermatogenesis in C. elegans. Genes Dev. 14: 2596-2609.
    • (2000) Genes Dev , vol.14 , pp. 2596-2609
    • Luitjens, C.1    Gallegos, M.2    Kraemer, B.3    Kimble, J.4    Wickens, M.5
  • 31
    • 84897507695 scopus 로고    scopus 로고
    • Characterisation of Caenorhabditis elegans sperm transcriptome and proteome
    • Ma, X., Y. Zhu, C. Li, P. Xue, Y. Zhao et al., 2014 Characterisation of Caenorhabditis elegans sperm transcriptome and proteome. BMC Genomics 15: 168.
    • (2014) BMC Genomics , vol.15 , pp. 168
    • Ma, X.1    Zhu, Y.2    Li, C.3    Xue, P.4    Zhao, Y.5
  • 32
    • 77956873635 scopus 로고    scopus 로고
    • The C elegans adult male germline: Stem cells and sexual dimorphism
    • Morgan, D. E., S. L. Crittenden, and J. Kimble, 2010 The C. elegans adult male germline: Stem cells and sexual dimorphism. Dev. Biol. 346: 204-214.
    • (2010) Dev. Biol , vol.346 , pp. 204-214
    • Morgan, D.E.1    Crittenden, S.L.2    Kimble, J.3
  • 33
    • 0026088664 scopus 로고
    • Molecular analysis of tra-2, a sex determining gene in Caenorhabditis elegans
    • Okkema, P. G., and J. Kimble, 1991 Molecular analysis of tra-2, a sex determining gene in Caenorhabditis elegans. EMBO J. 10: 171-176.
    • (1991) EMBO J , vol.10 , pp. 171-176
    • Okkema, P.G.1    Kimble, J.2
  • 34
    • 0033019053 scopus 로고    scopus 로고
    • The Caenorhabditis elegans sex determination gene mog-1 encodes a member of the DEAH-box protein family
    • Puoti, A., and J. Kimble, 1999 The Caenorhabditis elegans sex determination gene mog-1 encodes a member of the DEAH-box protein family. Mol. Cell. Biol. 19: 2189-2197.
    • (1999) Mol. Cell. Biol , vol.19 , pp. 2189-2197
    • Puoti, A.1    Kimble, J.2
  • 35
    • 0034724183 scopus 로고    scopus 로고
    • The hermaphrodite sperm/oocyte switch requires the Caenorhabditis elegans homologs of PRP2 and PRP22
    • Puoti, A., and J. Kimble, 2000 The hermaphrodite sperm/oocyte switch requires the Caenorhabditis elegans homologs of PRP2 and PRP22. Proc. Natl. Acad. Sci. USA 97: 3276-3281.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 3276-3281
    • Puoti, A.1    Kimble, J.2
  • 36
    • 84883644707 scopus 로고    scopus 로고
    • Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
    • Rapaport, F., R. Khanin, Y. Liang, M. Pirun, A. Krek et al., 2013 Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol. 14: R95.
    • (2013) Genome Biol , vol.14 , pp. R95
    • Rapaport, F.1    Khanin, R.2    Liang, Y.3    Pirun, M.4    Krek, A.5
  • 37
    • 0842344618 scopus 로고    scopus 로고
    • Genome-wide germlineenriched and sex-biased expression profiles in Caenorhabditis elegans
    • Reinke, V., I. S. Gil, S. Ward, and K. Kazmer, 2004 Genome-wide germlineenriched and sex-biased expression profiles in Caenorhabditis elegans. Development 131: 311-323.
    • (2004) Development , vol.131 , pp. 311-323
    • Reinke, V.1    Gil, I.S.2    Ward, S.3    Kazmer, K.4
  • 38
    • 0033639116 scopus 로고    scopus 로고
    • A global profile of germline gene expression in C elegans.
    • Reinke, V., H. E. Smith, J. Nance, J. Wang, C. Van Doren et al., 2000 A global profile of germline gene expression in C. elegans. Mol. Cell 6: 605-616.
    • (2000) Mol. Cell , vol.6 , pp. 605-616
    • Reinke, V.1    Smith, H.E.2    Nance, J.3    Wang, J.4    Van Doren, C.5
  • 39
    • 84879232999 scopus 로고    scopus 로고
    • Chromosome pairing and synapsis during Caenorhabditis elegans meiosis
    • Rog, O., and A. F. Dernburg, 2013 Chromosome pairing and synapsis during Caenorhabditis elegans meiosis. Curr. Opin. Cell Biol. 25: 349-356.
    • (2013) Curr. Opin. Cell Biol , vol.25 , pp. 349-356
    • Rog, O.1    Dernburg, A.F.2
  • 40
    • 0024003259 scopus 로고
    • fog-2, a germ-line-specific sex determination gene required for hermaphrodite spermatogenesis in Caenorhabditis elegans
    • Schedl, T., and J. Kimble, 1988 fog-2, a germ-line-specific sex determination gene required for hermaphrodite spermatogenesis in Caenorhabditis elegans. Genetics 119: 43-61.
    • (1988) Genetics , vol.119 , pp. 43-61
    • Schedl, T.1    Kimble, J.2
  • 41
    • 0032529361 scopus 로고    scopus 로고
    • Genetic requirements for PIE-1 localization and inhibition of gene expression in the embryonic germ lineage of Caenorhabditis elegans
    • Tenenhaus, C., C. Schubert, and G. Seydoux, 1998 Genetic requirements for PIE-1 localization and inhibition of gene expression in the embryonic germ lineage of Caenorhabditis elegans. Dev. Biol. 200: 212-224.
    • (1998) Dev. Biol , vol.200 , pp. 212-224
    • Tenenhaus, C.1    Schubert, C.2    Seydoux, G.3
  • 42
    • 84869507315 scopus 로고    scopus 로고
    • Simplification and desexualization of gene expression in selffertile nematodes
    • Thomas, C. G., R. Li, H. E. Smith, G. C. Woodruff, B. Oliver et al., 2012 Simplification and desexualization of gene expression in selffertile nematodes. Curr. Biol. 22: 2167-2172.
    • (2012) Curr. Biol , vol.22 , pp. 2167-2172
    • Thomas, C.G.1    Li, R.2    Smith, H.E.3    Woodruff, G.C.4    Oliver, B.5
  • 43
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell, C., A. Roberts, L. Goff, G. Pertea, D. Kim et al., 2012 Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7: 562-578.
    • (2012) Nat. Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5
  • 44
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C., B. A. Williams, G. Pertea, A. Mortazavi, G. Kwan et al., 2010 Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28: 511-515.
    • (2010) Nat. Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5
  • 45
    • 66349103355 scopus 로고    scopus 로고
    • Identification of genes expressed in the hermaphrodite germ line of C elegans using SAGE.
    • Wang, X., Y. Zhao, K. Wong, P. Ehlers, Y. Kohara et al., 2009 Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE. BMC Genomics 10: 213.
    • (2009) BMC Genomics , vol.10 , pp. 213
    • Wang, X.1    Zhao, Y.2    Wong, K.3    Ehlers, P.4    Kohara, Y.5
  • 46
    • 0022469499 scopus 로고
    • Monoclonal antibodies that recognize a polypeptide antigenic determinant shared by multiple Caenorhabditis elegans sperm-specific proteins
    • Ward, S., T. M. Roberts, S. Strome, F. M. Pavalko, and E. Hogan, 1986 Monoclonal antibodies that recognize a polypeptide antigenic determinant shared by multiple Caenorhabditis elegans sperm-specific proteins. J. Cell Biol. 102: 1778-1786.
    • (1986) J. Cell Biol , vol.102 , pp. 1778-1786
    • Ward, S.1    Roberts, T.M.2    Strome, S.3    Pavalko, F.M.4    Hogan, E.5
  • 48
    • 0033200331 scopus 로고    scopus 로고
    • Synapsis and chiasma formation in Caenorhabditis elegans require HIM-3, a meiotic chromosome core component that functions in chromosome segregation
    • Zetka, M. C., I. Kawasaki, S. Strome, and F. Müller, 1999 Synapsis and chiasma formation in Caenorhabditis elegans require HIM-3, a meiotic chromosome core component that functions in chromosome segregation. Genes Dev. 13: 2258-2270.
    • (1999) Genes Dev , vol.13 , pp. 2258-2270
    • Zetka, M.C.1    Kawasaki, I.2    Strome, S.3    Müller, F.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.