Deep sequencing-based expression analysis shows major advanc(5)

2018-12-17 14:28

Supplementary Data are available at NAR Online.

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION SUPPLEMENTARY DATA FUNDING REFERENCES TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION SUPPLEMENTARY DATA FUNDING REFERENCES FUNDING The Netherlands Genomics Initiative/Netherlands Organization for

Scientific Research (NGI/NWO); a VENI-grant from the Dutch Organization for Scientific Research (NWO grant 2005/03808/ALW to P.A.C.’tH.).

Conflict of interest statement. None declared.

ACKNOWLEDGEMENTS

We would like to thank Irina Khrebtukova and Gary Schroth (Illumina Inc., Hayward,CA) for sample preparation protocols, analysis of the pooled samples and assistance with data analysis. Michiel van Galen and Mattias den Hollander (LUMC and Hogeschool Leiden) are acknowledged for skillful assistance in bioinformatics. We would like to thank Jelle Goeman for

helpful comments and Prof. Silvère van der Maarel and Prof. Rune Frants for critically reading the manuscript.

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION SUPPLEMENTARY DATA FUNDING REFERENCES REFERENCES 1. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, et al.

Multiple-laboratory comparison of microarray platforms. Nat. Methods (2005) 2:345–350.[CrossRef][Web of Science][Medline] 2. Harbers M, Carninci P. Tag-based approaches for transcriptome research and genome annotation. Nat. Methods (2005) 2:495–502.[CrossRef][Web of Science][Medline] 3. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. (2000) 18:630–634.[CrossRef][Web of Science][Medline] 4. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 437:376–380.[Web of Science][Medline] 5. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. Accurate multiplex polony

sequencing of an evolved bacterial genome. Science (2005) 309:1728–1732.[Abstract/Free Full Text]

6. Bentley DR. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. (2006) 16:545–552.[CrossRef][Web of Science][Medline] 7. Jongeneel CV, Iseli C, Stevenson BJ, Riggins GJ, Lal A, Mackay A, Harris RA, O’Hare MJ, Neville AM, Simpson AJ, et al. Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc. Natl Acad. Sci. USA (2003) 100:4702–4705.[Abstract/Free Full Text] 8. Engels BM, Schouten TG, van Dullemen J, Gosens I, Vreugdenhil E. Functional differences between two DCLK splice variants. Brain Res. Mol. Brain Res. (2004) 120:103–114.[Medline] 9. Pedotti P, 't Hoen PA, Vreugdenhil E, Schenk GJ, Vossen RH, Ariyurek Y, de Hollander M, Kuiper R, van Ommen GJ, den Dunnen JT, et al. Can subtle changes in gene expression be consistently detected with different microarray platforms? BMC. Genomics (2008) 9:124.[CrossRef][Medline] 10.Vencio RZ, Brentani H, Patrao DF, Pereira CA. Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE). BMC. Bioinformatics. (2004) 5:119.[CrossRef][Medline] 11.Goeman JJ, van de Geer SA, de Kort F, van Houwelingen HC. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics. (2004)

20:93–99.[Abstract/Free Full Text] 12.Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ, Beaudry GA, Ciriello KM, et al. Analysis of human transcriptomes. Nat. Genet. (1999) 23:387–388.[Web of Science][Medline] 13.Pauws E, van Kampen AH, van de Graaf SA, de Vijlder JJ, Ris-Stalpers C. Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. Nucleic Acids Res. (2001) 29:1690–1694.[Abstract/Free Full Text] 14.Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D. Patterns of variant polyadenylation signal usage in human genes. Genome Res. (2000) 10:1001–1010.[Abstract/Free Full Text]

15.Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R, et al. Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. (2003) 21:379–386.[CrossRef][Web of Science][Medline] 16.Ge X, Wu Q, Jung YC, Chen J, Wang SM. A large quantity of novel human antisense transcripts detected by LongSAGE. Bioinformatics. (2006) 22:2475–2479.[Abstract/Free Full Text] 17.Werner A, Schmutzler G, Carlile M, Miles CG, Peters H. Expression profiling of antisense transcripts on DNA arrays. Physiol. Genomics (2007) 28:294–300.[Abstract/Free Full Text] 18.Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al. Antisense transcription in the mammalian transcriptome. Science (2005) 309:1564–1566.[Abstract/Free Full Text] 19.Sun M, Hurst LD, Carmichael GG, Chen J. Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. Genome Res. (2006)

16:922–933.[Abstract/Free Full Text] 20.Perocchi F, Xu Z, Clauder-Munster S, Steinmetz LM. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res. (2007) 35:e128.[Abstract/Free Full Text] 21.Ruijter JM, van Kampen AH, Baas F. Statistical evaluation of SAGE libraries: consequences for experimental design. Physiol. Genomics (2002) 11:37–44.[Abstract/Free Full Text] 22.Snedecor GW, Cochran WG. Square root transformation for counts. In: Statistical Methods.—Cochran WG, ed. (1989) Hoboken, NJ: Blackwell Publishing. 287–288. 23.Lin PT, Gleeson JG, Corbo JC, Flanagan L, Walsh CA. DCAMKL1 encodes a protein kinase with homology to doublecortin that regulates microtubule polymerization. J. Neurosci. (2000) 20:9152–9161.[Abstract/Free Full Text] 24.Deuel TA, Liu JS, Corbo JC, Yoo SY, Rorke-Adams LB, Walsh CA. Genetic interactions between doublecortin and doublecortin-like kinase in

neuronal migration and axon outgrowth. Neuron (2006) 49:41–53.[CrossRef][Web of Science][Medline]

25.Shang L, Kwon YG, Nandy S, Lawrence DS, Edelman AM. Catalytic and regulatory domains of doublecortin kinase-1. Biochemistry (2003) 42:2185–2194.[CrossRef][Web of Science][Medline] 26.Feldker DE, Datson NA, Veenema AH, Proutski V, Lathouwers D, de Kloet ER, Vreugdenhil E. GeneChip analysis of hippocampal gene expression profiles of short- and long-attack-latency mice: technical and biological implications. J. Neurosci. Res. (2003) 74:701–716.[CrossRef][Web of Science][Medline] 27.Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al. Stem cell

transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods (2008) 5:613–619.[CrossRef][Web of Science][Medline] 28.Marioni J, Mason C, Mane S, Stephens M, Gilad Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. (2008) 18:1509–1517.[Abstract/Free Full Text] 29.Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bahler J. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 453:1239–1243.[CrossRef][Web of Science][Medline] 30.Lu J, Lal A, Merriman B, Nelson S, Riggins G. A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips. Genomics (2004) 84:631–636.[CrossRef][Web of Science][Medline] 31.Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL, Ohno-Machado L, Hovig E, Patrick KW. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics (2007) 8:153.[CrossRef][Medline] 32.Smyth GK. Limma: linear models for microarray data. In:

Bioinformatics and Computational Biology Solutions Using R and Bioconductor.—Gentleman RC, Carey VJ, Dudoit S, Irizarry R, Huber W, eds. (2005) New York: Springer. 397–420. 33.Nielsen KL, Hogh AL, Emmersen J. DeepSAGE–digital transcriptomics with high sensitivity, simple experimental protocol and


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