메뉴 건너뛰기




Volumn 16, Issue 1, 2015, Pages

Generation of a de novo transcriptome from equine lamellar tissue

Author keywords

Assembly; Equine; Laminitis; RNA seq; Transcriptome

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

EID: 84943586437     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1948-8     Document Type: Article
Times cited : (13)

References (55)
  • 1
    • 77950347636 scopus 로고    scopus 로고
    • The anatomy and physiology of the suspensory apparatus of the distal phalanx
    • Pollitt CC. The anatomy and physiology of the suspensory apparatus of the distal phalanx. Vet Clin North Am Equine Pract. 2010;26(1):29-49.
    • (2010) Vet Clin North Am Equine Pract , vol.26 , Issue.1 , pp. 29-49
    • Pollitt, C.C.1
  • 2
    • 77950365442 scopus 로고    scopus 로고
    • Overview of current laminitis research
    • Eades SC. Overview of current laminitis research. Vet Clin North Am Equine Pract. 2010;26(1):51-63.
    • (2010) Vet Clin North Am Equine Pract , vol.26 , Issue.1 , pp. 51-63
    • Eades, S.C.1
  • 3
    • 84905566949 scopus 로고    scopus 로고
    • Continuous digital hypothermia initiated after the onset of lameness prevents lamellar failure in the oligofructose laminitis model
    • van Eps AW, Pollitt CC, Underwood C, Medina-Torres CE, Goodwin WA, Belknap JK. Continuous digital hypothermia initiated after the onset of lameness prevents lamellar failure in the oligofructose laminitis model. Equine Vet J. 2014;46(5):625-30.
    • (2014) Equine Vet J , vol.46 , Issue.5 , pp. 625-630
    • Eps, A.W.1    Pollitt, C.C.2    Underwood, C.3    Medina-Torres, C.E.4    Goodwin, W.A.5    Belknap, J.K.6
  • 4
    • 80052498907 scopus 로고    scopus 로고
    • National Economic Cost of Equine Lameness, Colic, and Equine Protozoal Myeloencephalitis (EPM) in the United States
    • Fort Collins: U.S. Department of Agriculture, APHIS;
    • Service USAaPHI, System NAHM. National Economic Cost of Equine Lameness, Colic, and Equine Protozoal Myeloencephalitis (EPM) in the United States. Fort Collins: U.S. Department of Agriculture, APHIS; 2001.
    • (2001)
  • 7
    • 78650103320 scopus 로고    scopus 로고
    • Laminar inflammatory gene expression in the carbohydrate overload model of equine laminitis
    • Leise BS, Faleiros RR, Watts M, Johnson PJ, Black SJ, Belknap JK. Laminar inflammatory gene expression in the carbohydrate overload model of equine laminitis. Equine Vet J. 2011;43(1):54-61.
    • (2011) Equine Vet J , vol.43 , Issue.1 , pp. 54-61
    • Leise, B.S.1    Faleiros, R.R.2    Watts, M.3    Johnson, P.J.4    Black, S.J.5    Belknap, J.K.6
  • 8
    • 84881026599 scopus 로고    scopus 로고
    • Disparate effects of LPS infusion and carbohydrate overload on inflammatory gene expression in equine laminae
    • Kwon S, Moore JN, Robertson TP, Hurley DJ, Wagner B, Vandenplas ML. Disparate effects of LPS infusion and carbohydrate overload on inflammatory gene expression in equine laminae. Vet Immunol Immunopathol. 2013;155(1-2):1-8.
    • (2013) Vet Immunol Immunopathol , vol.155 , Issue.1-2 , pp. 1-8
    • Kwon, S.1    Moore, J.N.2    Robertson, T.P.3    Hurley, D.J.4    Wagner, B.5    Vandenplas, M.L.6
  • 10
    • 84873551927 scopus 로고    scopus 로고
    • Impact of laminitis on the canonical Wnt signaling pathway in basal epithelial cells of the equine digital laminae
    • Wang L, Pawlak EA, Johnson PJ, Belknap JK, Eades S, Stack S, et al. Impact of laminitis on the canonical Wnt signaling pathway in basal epithelial cells of the equine digital laminae. PLoS One. 2013;8(2):e56025.
    • (2013) PLoS One , vol.8 , Issue.2 , pp. e56025
    • Wang, L.1    Pawlak, E.A.2    Johnson, P.J.3    Belknap, J.K.4    Eades, S.5    Stack, S.6
  • 11
    • 84892488310 scopus 로고    scopus 로고
    • Expression and activity of collagenases in the digital laminae of horses with carbohydrate overload-induced acute laminitis
    • Wang L, Pawlak EA, Johnson PJ, Belknap JK, Alfandari D, Black SJ. Expression and activity of collagenases in the digital laminae of horses with carbohydrate overload-induced acute laminitis. J Vet Intern Med. 2014;28(1):215-22.
    • (2014) J Vet Intern Med , vol.28 , Issue.1 , pp. 215-222
    • Wang, L.1    Pawlak, E.A.2    Johnson, P.J.3    Belknap, J.K.4    Alfandari, D.5    Black, S.J.6
  • 12
    • 68549140126 scopus 로고    scopus 로고
    • Gene expression in the lamellar dermis-epidermis during the developmental phase of carbohydrate overload-induced laminitis in the horse
    • Budak MT, Orsini JA, Pollitt CC, Rubinstein NA. Gene expression in the lamellar dermis-epidermis during the developmental phase of carbohydrate overload-induced laminitis in the horse. Vet Immunol Immunopathol. 2009;131(1-2):86-96.
    • (2009) Vet Immunol Immunopathol , vol.131 , Issue.1-2 , pp. 86-96
    • Budak, M.T.1    Orsini, J.A.2    Pollitt, C.C.3    Rubinstein, N.A.4
  • 13
    • 64749108301 scopus 로고    scopus 로고
    • Temporal aspects of laminar gene expression during the developmental stages of equine laminitis
    • Noschka E, Vandenplas ML, Hurley DJ, Moore JN. Temporal aspects of laminar gene expression during the developmental stages of equine laminitis. Vet Immunol Immunopathol. 2009;129(3-4):242-53.
    • (2009) Vet Immunol Immunopathol , vol.129 , Issue.3-4 , pp. 242-253
    • Noschka, E.1    Vandenplas, M.L.2    Hurley, D.J.3    Moore, J.N.4
  • 14
    • 78449303652 scopus 로고    scopus 로고
    • Structural annotation of equine protein-coding genes determined by mRNA sequencing
    • Coleman SJ, Zeng Z, Wang K, Luo S, Khrebtukova I, Mienaltowski MJ, et al. Structural annotation of equine protein-coding genes determined by mRNA sequencing. Anim Genet. 2010;41 Suppl 2:121-30.
    • (2010) Anim Genet , vol.41 , pp. 121-130
    • Coleman, S.J.1    Zeng, Z.2    Wang, K.3    Luo, S.4    Khrebtukova, I.5    Mienaltowski, M.J.6
  • 15
    • 84880787872 scopus 로고    scopus 로고
    • Analysis of unannotated equine transcripts identified by mRNA sequencing
    • Coleman SJ, Zeng Z, Hestand MS, Liu J, Macleod JN. Analysis of unannotated equine transcripts identified by mRNA sequencing. PLoS One. 2013;8(7):e70125.
    • (2013) PLoS One , vol.8 , Issue.7 , pp. e70125
    • Coleman, S.J.1    Zeng, Z.2    Hestand, M.S.3    Liu, J.4    Macleod, J.N.5
  • 16
    • 57149085481 scopus 로고    scopus 로고
    • Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    • 't Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 2008;36(21):e141.
    • (2008) Nucleic Acids Res , vol.36 , Issue.21 , pp. e141
    • 't Hoen, P.A.1    Ariyurek, Y.2    Thygesen, H.H.3    Vreugdenhil, E.4    Vossen, R.H.5    Menezes, R.X.6
  • 17
    • 79957665988 scopus 로고    scopus 로고
    • Microarrays, deep sequencing and the true measure of the transcriptome
    • Malone JH, Oliver B. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol. 2011;9:34.
    • (2011) BMC Biol , vol.9 , pp. 34
    • Malone, J.H.1    Oliver, B.2
  • 18
    • 84892752418 scopus 로고    scopus 로고
    • A novel splicing outcome reveals more than 2000 new mammalian protein isoforms
    • Wilson LO, Spriggs A, Taylor JM, Fahrer AM. A novel splicing outcome reveals more than 2000 new mammalian protein isoforms. Bioinformatics. 2014;30(2):151-6.
    • (2014) Bioinformatics , vol.30 , Issue.2 , pp. 151-156
    • Wilson, L.O.1    Spriggs, A.2    Taylor, J.M.3    Fahrer, A.M.4
  • 19
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008;18(9):1509-17.
    • (2008) Genome Res , vol.18 , Issue.9 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 20
    • 84875923909 scopus 로고    scopus 로고
    • Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris
    • Mooney M, Bond J, Monks N, Eugster E, Cherba D, Berlinski P, et al. Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris. PLoS One. 2013;8(4):e61088.
    • (2013) PLoS One , vol.8 , Issue.4 , pp. e61088
    • Mooney, M.1    Bond, J.2    Monks, N.3    Eugster, E.4    Cherba, D.5    Berlinski, P.6
  • 21
    • 84898618335 scopus 로고    scopus 로고
    • Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells
    • Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One. 2014;9(1), e78644.
    • (2014) PLoS One , vol.9 , Issue.1
    • Zhao, S.1    Fung-Leung, W.P.2    Bittner, A.3    Ngo, K.4    Liu, X.5
  • 22
    • 84866026429 scopus 로고    scopus 로고
    • Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq
    • Park KD, Park J, Ko J, Kim BC, Kim HS, Ahn K, et al. Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq. BMC Genomics. 2012;13:473.
    • (2012) BMC Genomics , vol.13 , pp. 473
    • Park, K.D.1    Park, J.2    Ko, J.3    Kim, B.C.4    Kim, H.S.5    Ahn, K.6
  • 24
  • 25
    • 81555234540 scopus 로고    scopus 로고
    • iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences
    • Zheng Y, Zhao L, Gao J, Fei Z. iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics. 2011;12:453.
    • (2011) BMC Bioinformatics , vol.12 , pp. 453
    • Zheng, Y.1    Zhao, L.2    Gao, J.3    Fei, Z.4
  • 26
    • 85019192202 scopus 로고    scopus 로고
    • NAGRP Host of Supplementary Data to Publications. http://www.animalgenome.org/repository/pub/CORNEL2015.0126/ ]
  • 27
    • 70449379045 scopus 로고    scopus 로고
    • Genome sequence, comparative analysis, and population genetics of the domestic horse
    • Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, et al. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science. 2009;326(5954):865-7.
    • (2009) Science , vol.326 , Issue.5954 , pp. 865-867
    • Wade, C.M.1    Giulotto, E.2    Sigurdsson, S.3    Zoli, M.4    Gnerre, S.5    Imsland, F.6
  • 28
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303.
    • (2010) Genome Res , vol.20 , Issue.9 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3    Sivachenko, A.4    Cibulskis, K.5    Kernytsky, A.6
  • 29
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43(5):491-8.
    • (2011) Nat Genet , vol.43 , Issue.5 , pp. 491-498
    • DePristo, M.A.1    Banks, E.2    Poplin, R.3    Garimella, K.V.4    Maguire, J.R.5    Hartl, C.6
  • 30
    • 84896009017 scopus 로고    scopus 로고
    • From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline
    • Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;11(1110):11.10.11-33.
    • (2013) Curr Protoc Bioinformatics , vol.11 , Issue.1110 , pp. 1110-1133
    • Auwera, G.A.1    Carneiro, M.O.2    Hartl, C.3    Poplin, R.4    Angel, G.5    Levy-Moonshine, A.6
  • 31
    • 85019211958 scopus 로고    scopus 로고
    • Horse Genome Analysis Data Repository. [http://www.animalgenome.org/repository/horse/]
  • 32
    • 84943582468 scopus 로고    scopus 로고
    • UNIX and Perl to the Rescue!: A Field Guide for the Life Sciences (and Other Data-rich Pursuits). Cambridge: Cambridge University Press;
    • Bradnam K, Korf I. UNIX and Perl to the Rescue!: A Field Guide for the Life Sciences (and Other Data-rich Pursuits). Cambridge: Cambridge University Press; 2012.
    • (2012)
    • Bradnam, K.1    Korf, I.2
  • 35
    • 84871402707 scopus 로고    scopus 로고
    • Identification and comparative analysis of ncRNAs in human, mouse and zebrafish indicate a conserved role in regulation of genes expressed in brain
    • Qu Z, Adelson DL. Identification and comparative analysis of ncRNAs in human, mouse and zebrafish indicate a conserved role in regulation of genes expressed in brain. PLoS One. 2012;7(12):e52275.
    • (2012) PLoS One , vol.7 , Issue.12 , pp. e52275
    • Qu, Z.1    Adelson, D.L.2
  • 36
    • 84943585364 scopus 로고    scopus 로고
    • Computational Approaches for the Analysis of ncRNA through Deep Sequencing Techniques
    • Veneziano D, Nigita G, Ferro A. Computational Approaches for the Analysis of ncRNA through Deep Sequencing Techniques. Front Bioeng Biotechnol. 2015;3:77.
    • (2015) Front Bioeng Biotechnol , vol.3 , pp. 77
    • Veneziano, D.1    Nigita, G.2    Ferro, A.3
  • 37
    • 77952905505 scopus 로고    scopus 로고
    • Most "dark matter" transcripts are associated with known genes
    • van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Most "dark matter" transcripts are associated with known genes. PLoS Biol. 2010;8(5):e1000371.
    • (2010) PLoS Biol , vol.8 , Issue.5 , pp. e1000371
    • Bakel, H.1    Nislow, C.2    Blencowe, B.J.3    Hughes, T.R.4
  • 38
    • 84870238817 scopus 로고    scopus 로고
    • Dark Matter RNA: Existence, Function, and Controversy
    • Kapranov P, St Laurent G. Dark Matter RNA: Existence, Function, and Controversy. Front Genet. 2012;3:60.
    • (2012) Front Genet , vol.3 , pp. 60
    • Kapranov, P.1    St Laurent, G.2
  • 39
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012;81:145-66.
    • (2012) Annu Rev Biochem , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 40
    • 84868683051 scopus 로고    scopus 로고
    • Regulation of mammalian cell differentiation by long non-coding RNAs
    • Hu W, Alvarez-Dominguez JR, Lodish HF. Regulation of mammalian cell differentiation by long non-coding RNAs. EMBO Rep. 2012;13(11):971-83.
    • (2012) EMBO Rep , vol.13 , Issue.11 , pp. 971-983
    • Hu, W.1    Alvarez-Dominguez, J.R.2    Lodish, H.F.3
  • 41
    • 84867070330 scopus 로고    scopus 로고
    • Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes
    • Morán I, Akerman I, van de Bunt M, Xie R, Benazra M, Nammo T, et al. Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes. Cell Metab. 2012;16(4):435-48.
    • (2012) Cell Metab , vol.16 , Issue.4 , pp. 435-448
    • Morán, I.1    Akerman, I.2    Bunt, M.3    Xie, R.4    Benazra, M.5    Nammo, T.6
  • 42
    • 84878025706 scopus 로고    scopus 로고
    • Novel insights into the bovine polled phenotype and horn ontogenesis in Bovidae
    • Allais-Bonnet A, Grohs C, Medugorac I, Krebs S, Djari A, Graf A, et al. Novel insights into the bovine polled phenotype and horn ontogenesis in Bovidae. PLoS One. 2013;8(5):e63512.
    • (2013) PLoS One , vol.8 , Issue.5 , pp. e63512
    • Allais-Bonnet, A.1    Grohs, C.2    Medugorac, I.3    Krebs, S.4    Djari, A.5    Graf, A.6
  • 43
    • 70349866687 scopus 로고    scopus 로고
    • ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
    • Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics. 2009;25(19):2607-8.
    • (2009) Bioinformatics , vol.25 , Issue.19 , pp. 2607-2608
    • Morgan, M.1    Anders, S.2    Lawrence, M.3    Aboyoun, P.4    Pagès, H.5    Gentleman, R.6
  • 44
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589-95.
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 46
    • 0036226603 scopus 로고    scopus 로고
    • BLAT--the BLAST-like alignment tool
    • Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002;12(4):656-64.
    • (2002) Genome Res , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1
  • 48
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841-2.
    • (2010) Bioinformatics , vol.26 , Issue.6 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 51
    • 84943581459 scopus 로고    scopus 로고
    • RepeatMasker Open-3.0. In: 1996-2010
    • Smit A, Hubley R, Green P. RepeatMasker Open-3.0. In: 1996-2010: http://www.repeatmasker.org/.
    • Smit, A.1    Hubley, R.2    Green, P.3
  • 54
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000;132:365-86.
    • (2000) Methods Mol Biol , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 55
    • 0031955116 scopus 로고    scopus 로고
    • Consed: a graphical tool for sequence finishing
    • Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res. 1998;8(3):195-202.
    • (1998) Genome Res , vol.8 , Issue.3 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.