Comparison between normalised and unnormalised 454-sequencing libraries for small-scale RNA-Seq studies

Comparative and Functional Genomics

Volumn 2012, Issue , 2012, Pages

  Ekblom, Robert ^a,b   Slate, Jon ^b   Horsburgh, Gavin J ^b   Birkhead, Tim ^b   Burke, Terry ^b  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; MICROSATELLITE DNA;

ANIMAL EXPERIMENT; ARTICLE; BLOOD; COMPARATIVE STUDY; DNA LIBRARY; GENE EXPRESSION; GENE SEQUENCE; MALE; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPLEEN;

TAENIOPYGIA GUTTATA;

EID: 84858116755     PISSN: 15316912     EISSN: 15326268     Source Type: Journal    
DOI: 10.1155/2012/281693     Document Type: Article

References (38)

1. Ekblom R., Galindo J., Applications of next generation sequencing in molecular ecology of non-model organisms Heredity 2011 107 1 1 15
2. Hudson M. E., Sequencing breakthroughs for genomic ecology and evolutionary biology Molecular Ecology Resources 2008 8 1 3 17 (Pubitemid 350231221)
3. Shendure J., Ji H., Next-generation DNA sequencing Nature Biotechnology 2008 26 10 1135 1145
4. Wang Z., Gerstein M., Snyder M., RNA-Seq: a revolutionary tool for transcriptomics Nature Reviews Genetics 2009 10 1 57 63
5. 't Hoen P. A. C., Ariyurek Y., Thygesen H. H., Vreugdenhil E., Vossen R. H. A. M., de Menezes R. X., Boer J. M., van Ommen G. J. B., den Dunnen J. T., Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms Nucleic Acids Research 2008 36 21, article no. e141
6. Wolf J. B. W., Bayer T., Haubold B., Schilhabel M., Rosenstiel P., Tautz D., Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow Molecular Ecology 2010 19 1 162 175
7. Ouborg N. J., Pertoldi C., Loeschcke V., Bijlsma R. K., Hedrick P. W., Conservation genetics in transition to conservation genomics Trends in Genetics 2010 26 4 177 187
8. Meyer E., Aglyamova G. V., Matz M. V., Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure Molecular Ecology 2011 20 17 3599 3616
9. Everett M. V., Grau E. D., Seeb J. E., Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome Molecular Ecology Resources 2011 11 supplement 1 93 108
10. Wang Z., Fang B., Chen J., Zhang X., Luo Z., Huang L., Chen X., Li Y., De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) BMC Genomics 2010 11 1, article no. 726
11. Wheat C. W., Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing Genetica 2010 138 4 433 451
12. Der J. P., Barker M. S., Wickett N. J., dePamphilis C. W., Wolf P. G., De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum BMC Genomics 2011 12, article 99
13. Kaur S., Cogan N. O. I., Pembleton L. W., Shinozuka M., Savin K. W., Materne M., Forster J. W., Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery BMC Genomics 2011 12, article 265
14. Vli U., Brandstrm M., Johansson M., Ellegren H., Insertion-deletion polymorphisms (indels) as genetic markers in natural populations BMC Genetics 2008 9, article 8
15. Buggs R. J. A., Chamala S., Wu W., Gao L., May G. D., Schnable P. S., Soltis D. E., Soltis P. S., Barbazuk W. B., Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping Molecular Ecology 2010 19 1 132 146
16. Barakat A., Diloreto D. S., Zhang Y., Smith C., Baier K., Powell W. A., Wheeler N., Sederoff R., Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection BMC Plant Biology 2009 9, article no. 51
17. Kristiansson E., Asker N., Frlin L., Joakim D. G. J., Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing BMC Genomics 2009 10, article no. 345
18. Zhulidov P. A., Bogdanova E. A., Shcheglov A. S., Vagner L. L., Khaspekov G. L., Kozhemyako V. B., Matz M. V., Meleshkevitch E., Moroz L. L., Lukyanov S. A., Shagin D. A., Simple cDNA normalization using kamchatka crab duplex-specific nuclease Nucleic Acids Research 2004 32 3, article e37
19. Bogdanova E. A., Shagina I. A., Mudrik E., Ivanov I., Amon P., Vagner L. L., Lukyanov S. A., Shagin D. A., DSN depletion is a simple method to remove selected transcripts from cDNA populations Molecular Biotechnology 2009 41 3 247 253
20. Hale M. C., McCormick C. R., Jackson J. R., DeWoody J. A., Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery BMC Genomics 2009 10, article no. 203
21. Yang P., Li X., Shipp M. J., Shockey J. M., Cahoon E. B., Mining the bitter melon (Momordica charantia L.) seed transcriptome by 454 analysis of non-normalized and normalized cDNA populations for conjugated fatty acid metabolism-related genes BMC Plant Biology 2010 10, article 250
22. Ewen-Campen B., Shaner N., Panfilio K. A., Suzuki Y., Roth S., Extavour C. G., The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus BMC Genomics 2011 12, article 61
23. Sun C., Li Y., Wu Q., Luo H., Sun Y., Song J., Lui E. M. K., Chen S., De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis BMC Genomics 2010 11, article 262
24. Stapley J., Birkhead T. R., Burke T., Slate J., A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution Genetics 2008 179 1 651 667
25. Altschul S. F., Madden T. L., Schffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Research 1997 25 17 3389 3402 (Pubitemid 27359211)
26. Flicek P., Amode M. R., Barrell D., Beal K., Brent S., Chen Y., Clapham P., Coates G., Fairley S., Fitzgerald S., Gordon L., Hendrix M., Hourlier T., Johnson N., K h ri A., Keefe D., Keenan S., Kinsella R., Kokocinski F., Kulesha E., Larsson P., Longden I., McLaren W., Overduin B., Pritchard B., Riat H. S., Rios D., Ritchie G. R.S., Ruffier M., Schuster M., Sobral D., Spudich G., Tang Y. A., Trevanion S., Vandrovcova J., Vilella A. J., White S., Wilder S. P., Zadissa A., Zamora J., Aken B. L., Birney E., Cunningham F., Dunham I., Durbin R., Fernndez-Suarez X. M., Herrero J., Hubbard T. J.P., Parker A., Proctor G., Vogel J., Searle S. M.J., Ensembl 2011 Nucleic Acids Research 2011 39 supplement 1 D800 D806
27. Smyth G., Gentleman R., Carey V. J., Huber W., Irizarry R. A., Dudoit S., Limma: Linear Models for Microarray Data Bioinformatics and Computational Biology Solutions Using R and Bioconductor 2005 New York, NY, USA Springer 397 420
28. R Development Core Team, R: A Language and Environment for Statistical Computing 2008 Vienna, Austria R Foundation for Statistical Computing
29. Gentleman R. C., Carey V. J., Bates D. M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A. J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J. Y., Zhang J., Bioconductor: open software development for computational biology and bioinformatics Genome Biology 2004 5 10, article R80
30. Robinson M. D., McCarthy D. J., Smyth G. K., edgeR: a bioconductor package for differential expression analysis of digital gene expression data Bioinformatics 2010 26 1 139 140
31. Benjamini Y., Hochberg Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing Journal of the Royal Statistical Society. Series B 1995 57 289 300
32. Faircloth B. C., MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design Molecular Ecology Resources 2008 8 1 92 94 (Pubitemid 350231173)
33. Ekblom R., Balakrishnan C. N., Burke T., Slate J., Digital gene expression analysis of the zebra finch genome BMC Genomics 2010 11 1, article no. 219
34. Schwarz D., Robertson H. M., Feder J. L., Varala K., Hudson M. E., Ragland G. J., Hahn D. A., Berlocher S. H., Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella BMC Genomics 2009 10, article no. 633
35. Cheung F., Win J., Lang J. M., Hamilton J., Vuong H., Leach J. E., Kamoun S., Lévesque C. A., Tisserat N., Buell C. R., Analysis of the Pythium ultimum transcriptome using Sanger and pyrosequencing approaches BMC Genomics 2008 9, article no. 542
36. Hahn D. A., Ragland G. J., Shoemaker D. D., Denlinger D. L., Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis BMC Genomics 2009 10, article no. 234
37. Primmer C. R., From conservation genetics to conservation genomics Annals of the New York Academy of Sciences 2009 1162 357 368
38. Parchman T. L., Geist K. S., Grahnen J. A., Benkman C. W., Buerkle C. A., Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery BMC Genomics 2010 11 1, article no. 180