메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA

Author keywords

[No Author keywords available]

Indexed keywords

CELL SURFACE RECEPTOR; G PROTEIN COUPLED RECEPTOR; GLOBIN; OLIGONUCLEOTIDE; RNA;

EID: 84855893655     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-28     Document Type: Article
Times cited : (51)

References (31)
  • 1
    • 58549118937 scopus 로고    scopus 로고
    • Identifying blood biomarkers for mood disorders using convergent functional genomics
    • 10.1038/mp.2008.11, 18301394
    • Le-Niculescu H, Kurian SM, Yehyawi N, Dike C, Patel SD, Edenberg HJ, et al. Identifying blood biomarkers for mood disorders using convergent functional genomics. Mol Psychiatry 2009, 14:156-174. 10.1038/mp.2008.11, 18301394.
    • (2009) Mol Psychiatry , vol.14 , pp. 156-174
    • Le-Niculescu, H.1    Kurian, S.M.2    Yehyawi, N.3    Dike, C.4    Patel, S.D.5    Edenberg, H.J.6
  • 2
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • 10.1038/nbt1486, 18846087
    • Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26:1135-1145. 10.1038/nbt1486, 18846087.
    • (2008) Nat Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 3
    • 33751001777 scopus 로고    scopus 로고
    • DeepSAGE digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples
    • 10.1093/nar/gkl714, 1636492, 17028099
    • Nielsen KL, Hogh AL, Emmersen J. DeepSAGE digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucleic Acids Res 2006, 34:e133. 10.1093/nar/gkl714, 1636492, 17028099.
    • (2006) Nucleic Acids Res , vol.34
    • Nielsen, K.L.1    Hogh, A.L.2    Emmersen, J.3
  • 4
    • 77954959148 scopus 로고    scopus 로고
    • Power of deep sequencing and agilent microarray for gene expression profiling study
    • 10.1007/s12033-010-9249-6, 20432071
    • Feng L, Liu H, Liu Y, Lu Z, Guo G, Guo S, et al. Power of deep sequencing and agilent microarray for gene expression profiling study. Mol Biotechnol 2010, 45:101-110. 10.1007/s12033-010-9249-6, 20432071.
    • (2010) Mol Biotechnol , vol.45 , pp. 101-110
    • Feng, L.1    Liu, H.2    Liu, Y.3    Lu, Z.4    Guo, G.5    Guo, S.6
  • 5
    • 70350453743 scopus 로고    scopus 로고
    • Relative power and sample size analysis on gene expression profiling data
    • 10.1186/1471-2164-10-439, 2759969, 19758461
    • van Iterson M, 't Hoen PA, Pedotti P, Hooiveld GJ, Den Dunnen JT, Van Ommen GJ, et al. Relative power and sample size analysis on gene expression profiling data. BMC Genomics 2009, 10:439. 10.1186/1471-2164-10-439, 2759969, 19758461.
    • (2009) BMC Genomics , vol.10 , pp. 439
    • van Iterson, M.1    't Hoen, P.A.2    Pedotti, P.3    Hooiveld, G.J.4    Den Dunnen, J.T.5    Van Ommen, G.J.6
  • 6
    • 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,
    • (2008) Nucleic Acids Res
    • 't Hoen, P.A.1    Ariyurek, Y.2    Thygesen, H.H.3    Vreugdenhil, E.4    Vossen, R.H.5    de Menezes, R.X.6
  • 7
    • 12344281124 scopus 로고    scopus 로고
    • Gene expression profiling using RNA extracted from whole blood: technologies and clinical applications
    • 10.1586/14737159.5.1.43, 15723591
    • Pahl A. Gene expression profiling using RNA extracted from whole blood: technologies and clinical applications. Expert Rev Mol Diagn 2005, 5:43-52. 10.1586/14737159.5.1.43, 15723591.
    • (2005) Expert Rev Mol Diagn , vol.5 , pp. 43-52
    • Pahl, A.1
  • 9
    • 23344448837 scopus 로고    scopus 로고
    • Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease
    • 10.1073/pnas.0504921102, 1182457, 16043692
    • Borovecki F, Lovrecic L, Zhou J, Jeong H, Then F, Rosas HD, et al. Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease. PNAS 2005, 102:11023-11028. 10.1073/pnas.0504921102, 1182457, 16043692.
    • (2005) PNAS , vol.102 , pp. 11023-11028
    • Borovecki, F.1    Lovrecic, L.2    Zhou, J.3    Jeong, H.4    Then, F.5    Rosas, H.D.6
  • 10
    • 33646010307 scopus 로고    scopus 로고
    • Evaluating the comparability of gene expression in blood and brain
    • 10.1002/ajmg.b.30272, 16526044
    • Sullivan PF, Fan C, Perou CM. Evaluating the comparability of gene expression in blood and brain. Am J Med Genet B Neuropsychiatr Genet 2006, 141B:261-268. 10.1002/ajmg.b.30272, 16526044.
    • (2006) Am J Med Genet B Neuropsychiatr Genet , vol.141 B , pp. 261-268
    • Sullivan, P.F.1    Fan, C.2    Perou, C.M.3
  • 11
    • 70349330786 scopus 로고    scopus 로고
    • Disease signatures are robust across tissues and experiments
    • 2758720, 19756046
    • Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Disease signatures are robust across tissues and experiments. Mol Syst Biol 2009, 5:307. 2758720, 19756046.
    • (2009) Mol Syst Biol , vol.5 , pp. 307
    • Dudley, J.T.1    Tibshirani, R.2    Deshpande, T.3    Butte, A.J.4
  • 12
    • 33344454373 scopus 로고    scopus 로고
    • The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool
    • 10.1016/j.lab.2005.10.005, 16503242
    • Liew CC, Ma J, Tang HC, Zheng R, Dempsey AA. The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool. J Lab Clin Med 2006, 147:126-132. 10.1016/j.lab.2005.10.005, 16503242.
    • (2006) J Lab Clin Med , vol.147 , pp. 126-132
    • Liew, C.C.1    Ma, J.2    Tang, H.C.3    Zheng, R.4    Dempsey, A.A.5
  • 13
    • 0036936826 scopus 로고    scopus 로고
    • Improvement of molecular monitoring of residual disease in leukemias by bedside RNA stabilization
    • 10.1038/sj.leu.2402734, 12454744
    • Muller MC, Merx K, Weisser A, Kreil S, Lahaye T, Hehlmann R, et al. Improvement of molecular monitoring of residual disease in leukemias by bedside RNA stabilization. Leukemia 2002, 16:2395-2399. 10.1038/sj.leu.2402734, 12454744.
    • (2002) Leukemia , vol.16 , pp. 2395-2399
    • Muller, M.C.1    Merx, K.2    Weisser, A.3    Kreil, S.4    Lahaye, T.5    Hehlmann, R.6
  • 14
    • 2942735008 scopus 로고    scopus 로고
    • Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types
    • 10.1038/sj.tpj.6500240, 15037859
    • Debey S, Schoenbeck U, Hellmich M, Gathof BS, Pillai R, Zander T, et al. Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types. Pharmacogenomics J 2004, 4:193-207. 10.1038/sj.tpj.6500240, 15037859.
    • (2004) Pharmacogenomics J , vol.4 , pp. 193-207
    • Debey, S.1    Schoenbeck, U.2    Hellmich, M.3    Gathof, B.S.4    Pillai, R.5    Zander, T.6
  • 16
    • 33847108537 scopus 로고    scopus 로고
    • Quantification of relative changes in specific mRNAs from frozen whole blood - methodological considerations and clinical implications
    • 10.1515/CCLM.2007.035, 17311503
    • Ovstebo R, Lande K, Kierulf P, Haug KB. Quantification of relative changes in specific mRNAs from frozen whole blood - methodological considerations and clinical implications. Clin Chem Lab Med 2007, 45:171-176. 10.1515/CCLM.2007.035, 17311503.
    • (2007) Clin Chem Lab Med , vol.45 , pp. 171-176
    • Ovstebo, R.1    Lande, K.2    Kierulf, P.3    Haug, K.B.4
  • 17
    • 33947598182 scopus 로고    scopus 로고
    • Functional identity of genes detectable in expression profiling assays following globin mRNA reduction of peripheral blood samples
    • 10.1016/j.clinbiochem.2007.01.004, 17303101
    • Field LA, Jordan RM, Hadix JA, Dunn MA, Shriver CD, Ellsworth RE, et al. Functional identity of genes detectable in expression profiling assays following globin mRNA reduction of peripheral blood samples. Clin Biochem 2007, 40:499-502. 10.1016/j.clinbiochem.2007.01.004, 17303101.
    • (2007) Clin Biochem , vol.40 , pp. 499-502
    • Field, L.A.1    Jordan, R.M.2    Hadix, J.A.3    Dunn, M.A.4    Shriver, C.D.5    Ellsworth, R.E.6
  • 18
    • 61649109505 scopus 로고    scopus 로고
    • Gene expression profiling of whole blood: comparison of target preparation methods for accurate and reproducible microarray analysis
    • 10.1186/1471-2164-10-2, 2649161, 19123946
    • Vartanian K, Slottke R, Johnstone T, Casale A, Planck SR, Choi D, et al. Gene expression profiling of whole blood: comparison of target preparation methods for accurate and reproducible microarray analysis. BMC Genomics 2009, 10:2. 10.1186/1471-2164-10-2, 2649161, 19123946.
    • (2009) BMC Genomics , vol.10 , pp. 2
    • Vartanian, K.1    Slottke, R.2    Johnstone, T.3    Casale, A.4    Planck, S.R.5    Choi, D.6
  • 19
    • 39749133586 scopus 로고    scopus 로고
    • Characterization of globin RNA interference in gene expression profiling of whole-blood samples
    • 10.1373/clinchem.2007.093419, 18089658
    • Wright C, Bergstrom D, Dai HY, Marton M, Morris M, Tokiwa G, et al. Characterization of globin RNA interference in gene expression profiling of whole-blood samples. Clin Chem 2008, 54:396-405. 10.1373/clinchem.2007.093419, 18089658.
    • (2008) Clin Chem , vol.54 , pp. 396-405
    • Wright, C.1    Bergstrom, D.2    Dai, H.Y.3    Marton, M.4    Morris, M.5    Tokiwa, G.6
  • 20
    • 65449163005 scopus 로고    scopus 로고
    • A Practical Platform for Blood Biomarker Study by Using Global Gene Expression Profiling of Peripheral Whole Blood
    • Tian Z, Palmer N, Schmid P, Yao H, Galdzicki M, Berger B, et al. A Practical Platform for Blood Biomarker Study by Using Global Gene Expression Profiling of Peripheral Whole Blood. PLoS ONE 2009, 4.
    • (2009) PLoS ONE , vol.4
    • Tian, Z.1    Palmer, N.2    Schmid, P.3    Yao, H.4    Galdzicki, M.5    Berger, B.6
  • 21
    • 33646087412 scopus 로고    scopus 로고
    • A highly standardized, robust, and cost-effective method for genome-wide transcriptome analysis of peripheral blood applicable to large-scale clinical trials
    • 10.1016/j.ygeno.2005.11.010, 16387473
    • Debey S, Zander T, Brors B, Popov A, Eils R, Schultze JL. A highly standardized, robust, and cost-effective method for genome-wide transcriptome analysis of peripheral blood applicable to large-scale clinical trials. Genomics 2006, 87:653-664. 10.1016/j.ygeno.2005.11.010, 16387473.
    • (2006) Genomics , vol.87 , pp. 653-664
    • Debey, S.1    Zander, T.2    Brors, B.3    Popov, A.4    Eils, R.5    Schultze, J.L.6
  • 22
    • 39449121572 scopus 로고    scopus 로고
    • Normalization of full-length enriched cDNA
    • 10.1039/b715110c, 18437263
    • Bogdanova EA, Shagin DA, Lukyanov SA. Normalization of full-length enriched cDNA. Mol Biosyst 2008, 4:205-212. 10.1039/b715110c, 18437263.
    • (2008) Mol Biosyst , vol.4 , pp. 205-212
    • Bogdanova, E.A.1    Shagin, D.A.2    Lukyanov, S.A.3
  • 23
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • 10.1261/rna.5248604, 1370637, 15383676
    • Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA 2004, 10:1507-1517. 10.1261/rna.5248604, 1370637, 15383676.
    • (2004) RNA , vol.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegerich, R.4
  • 24
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang D, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang, D.1    Sherman, B.T.2    Lempicki, R.A.3
  • 25
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • 10.1038/nature03001, 15496913, Human Genome Sequencing Consortium
    • Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome. Nature 2004, 431:931-945. 10.1038/nature03001, 15496913, Human Genome Sequencing Consortium.
    • (2004) Nature , vol.431 , pp. 931-945
  • 26
    • 79955788276 scopus 로고    scopus 로고
    • Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature
    • 3051107, 21296742
    • Wright MW, Bruford EA. Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature. Hum Genomics 2011, 5:90-98. 3051107, 21296742.
    • (2011) Hum Genomics , vol.5 , pp. 90-98
    • Wright, M.W.1    Bruford, E.A.2
  • 27
    • 73949085491 scopus 로고    scopus 로고
    • Non-coding RNAs: regulators of disease
    • 10.1002/path.2638, 19882673
    • Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. Non-coding RNAs: regulators of disease. J Pathol 2010, 220:126-139. 10.1002/path.2638, 19882673.
    • (2010) J Pathol , vol.220 , pp. 126-139
    • Taft, R.J.1    Pang, K.C.2    Mercer, T.R.3    Dinger, M.4    Mattick, J.S.5
  • 28
    • 33751186521 scopus 로고    scopus 로고
    • Effects of globin mRNA reduction methods on gene expression profiles from whole blood
    • 10.2353/jmoldx.2006.060021, 1876175, 17065423
    • Liu J, Walter E, Stenger D, Thach D. Effects of globin mRNA reduction methods on gene expression profiles from whole blood. J Mol Diagn 2006, 8:551-558. 10.2353/jmoldx.2006.060021, 1876175, 17065423.
    • (2006) J Mol Diagn , vol.8 , pp. 551-558
    • Liu, J.1    Walter, E.2    Stenger, D.3    Thach, D.4
  • 30
    • 41149085992 scopus 로고    scopus 로고
    • Small-sample estimation of negative binomial dispersion, with applications to SAGE data
    • Robinson MD, Smyth GK. Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 2008, 9:321-332.
    • (2008) Biostatistics , vol.9 , pp. 321-332
    • Robinson, M.D.1    Smyth, G.K.2
  • 31
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • 10.1093/bioinformatics/btp616, 2796818, 19910308
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140. 10.1093/bioinformatics/btp616, 2796818, 19910308.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.