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Volumn 24, Issue 7, 2014, Pages 1157-1168

Quantifying ChIP-seq data: A spiking method providing an internal reference for sample-to-sample normalization

(40)  Bonhoure, Nicolas a   Bounova, Gergana a,b   Bernasconi, David a,b,d   Praz, Viviane a,b   Lammers, Fabienne a   Canella, Donatella a   Willis, Ian M c   Herr, Winship a   Hernandez, Nouria a   Delorenzi, Mauro a,b   Deplancke, Bart d   Desvergne, Béatrice a   Guex, Nicolas b   Naef, Felix d   Rougemont, Jacques d   Schibler, Ueli e   Andersin, Teemu e   Cousin, Pascal a   Gilardi, Federica a   Gos, Pascal e   more..


Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; HUMAN; LIVER HOMOGENATE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROCEDURES; QUALITY CONTROL; SAMPLING; SPIKE ADJUSTMENT PROCEDURE; STANDARD; ULTRASOUND; ANIMAL; BIOLOGY; GENETICS; METABOLISM; REPRODUCIBILITY; STANDARDS;

EID: 84904252718     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.168260.113     Document Type: Article
Times cited : (117)

References (35)
  • 1
    • 34249026300 scopus 로고    scopus 로고
    • High-Resolution Profiling of Histone Methylations in the Human Genome
    • DOI 10.1016/j.cell.2007.05.009, PII S0092867407006009
    • Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. 2007.High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837. (Pubitemid 46802390)
    • (2007) Cell , vol.129 , Issue.4 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.-Y.4    Schones, D.E.5    Wang, Z.6    Wei, G.7    Chepelev, I.8    Zhao, K.9
  • 2
    • 77952988986 scopus 로고    scopus 로고
    • Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells
    • Canella D, Praz V, Reina JH, Cousin P, Hernandez N. 2010. Defining the RNA polymerase III transcriptome: genome-wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res 20: 710-721.
    • (2010) Genome Res , vol.20 , pp. 710-721
    • Canella, D.1    Praz, V.2    Reina, J.H.3    Cousin, P.4    Hernandez, N.5
  • 4
    • 0035827649 scopus 로고    scopus 로고
    • Reconstitution of transcription from the human U6 small nuclear RNA promoter with eight recombinant polypeptides and a partially purified RNA polymerase III complex
    • Chong SS, Hu P, Hernandez N. 2001. Reconstitution of transcription from the human U6 small nuclear RNA promoter with eight recombinant polypeptides and a partially purified RNA polymerase III complex. J Biol Chem 276: 20727-20734.
    • (2001) J Biol Chem , vol.276 , pp. 20727-20734
    • Chong, S.S.1    Hu, P.2    Hernandez, N.3
  • 5
    • 46749128583 scopus 로고    scopus 로고
    • Regulation of RNA polymerase III transcription by Maf1 protein
    • Ciesla M, Boguta M. 2008. Regulation of RNA polymerase III transcription by Maf1 protein. Acta Biochim Pol 55: 215-225. (Pubitemid 351947536)
    • (2008) Acta Biochimica Polonica , vol.55 , Issue.2 , pp. 215-225
    • Ciesla, M.1    Boguta, M.2
  • 6
    • 14844318502 scopus 로고    scopus 로고
    • Two steps in Maf1-dependent repression of transcription by RNA polymerase III
    • DOI 10.1074/jbc.M412375200
    • Desai N, Lee J, Upadhya R, Chu Y, Moir RD, Willis IM. 2005. Two steps in Maf1-dependent repression of transcription by RNA polymerase III. J Biol Chem 280: 6455-6462. (Pubitemid 40341193)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.8 , pp. 6455-6462
    • Desai, N.1    Lee, J.2    Upadhya, R.3    Chu, Y.4    Moir, R.D.5    Willis, I.M.6
  • 8
    • 84855792253 scopus 로고    scopus 로고
    • A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements
    • Enroth S, Andersson CR, Andersson R, Wadelius C, Gustafsson MG, Komorowski J. 2012. A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements. Algorithm Mol Biol 7: 2.
    • (2012) Algorithm Mol Biol , vol.7 , pp. 2
    • Enroth, S.1    Andersson, C.R.2    Andersson, R.3    Wadelius, C.4    Gustafsson, M.G.5    Komorowski, J.6
  • 10
    • 33749252730 scopus 로고    scopus 로고
    • Transcription: Adjusting to Adversity by Regulating RNA Polymerase
    • DOI 10.1016/j.cub.2006.08.071, PII S0960982206021385
    • Geiduschek EP, Kassavetis GA. 2006. Transcription: adjusting to adversity by regulating RNA polymerase. Curr Biol 16: R849-R851. (Pubitemid 44486767)
    • (2006) Current Biology , vol.16 , Issue.19
    • Geiduschek, E.P.1    Kassavetis, G.A.2
  • 11
    • 84875246124 scopus 로고    scopus 로고
    • RNA polymerase III repression by the retinoblastoma tumor suppressor protein
    • Gjidoda A, Henry RW. 2013. RNA polymerase III repression by the retinoblastoma tumor suppressor protein. Biochim Biophys Acta 1829: 385-392.
    • (2013) Biochim Biophys Acta , vol.1829 , pp. 385-392
    • Gjidoda, A.1    Henry, R.W.2
  • 12
    • 35848963394 scopus 로고    scopus 로고
    • Regulation of RNA polymerase III transcription during mammalian cell growth
    • Goodfellow SJ, White RJ. 2007. Regulation of RNA polymerase III transcription during mammalian cell growth. Cell Cycle 6: 2323-2326. (Pubitemid 350058680)
    • (2007) Cell Cycle , vol.6 , Issue.19 , pp. 2323-2326
    • Goodfellow, S.J.1    White, R.J.2
  • 13
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • DOI 10.1126/science.1141319
    • Johnson DS, Mortazavi A, Myers RM, Wold B. 2007a. Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502. (Pubitemid 46906620)
    • (2007) Science , vol.316 , Issue.5830 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 14
    • 34247553679 scopus 로고    scopus 로고
    • Mammalian Maf1 Is a Negative Regulator of Transcription by All Three Nuclear RNA Polymerases
    • DOI 10.1016/j.molcel.2007.03.021, PII S1097276507001918
    • Johnson SS, Zhang C, Fromm J, Willis IM, Johnson DL. 2007b. Mammalian Maf1 is a negative regulator of transcription by all three nuclear RNA polymerases. Mol Cell 26: 367-379. (Pubitemid 46687096)
    • (2007) Molecular Cell , vol.26 , Issue.3 , pp. 367-379
    • Johnson, S.S.1    Zhang, C.2    Fromm, J.3    Willis, I.M.4    Johnson, D.L.5
  • 15
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments forDNA-binding proteins
    • Kharchenko PV, Tolstorukov MY, Park PJ. 2008. Design and analysis of ChIP-seq experiments forDNA-binding proteins. Nat Biotechnol 26: 1351-1359.
    • (2008) Nat Biotechnol , vol.26 , pp. 1351-1359
    • Kharchenko, P.V.1    Tolstorukov, M.Y.2    Park, P.J.3
  • 18
    • 79955564639 scopus 로고    scopus 로고
    • Measuring reproducibility of high-throughput experiments
    • Li QH, Brown JB, Huang HY, Bickel PJ. 2011. Measuring reproducibility of high-throughput experiments. Ann Appl Stat 5: 1752-1779.
    • (2011) Ann Appl Stat , vol.5 , pp. 1752-1779
    • Li, Q.H.1    Brown, J.B.2    Huang, H.Y.3    Bickel, P.J.4
  • 23
    • 33744512096 scopus 로고    scopus 로고
    • General Repression of RNA Polymerase III Transcription Is Triggered by Protein Phosphatase Type 2A-Mediated Dephosphorylation of Maf1
    • DOI 10.1016/j.molcel.2006.04.008, PII S109727650600253X
    • Oficjalska-Pham D, Harismendy O, Smagowicz WJ, Gonzalez de Peredo A, Boguta M, Sentenac A, Lefebvre O. 2006. General repression of RNA polymerase III transcription is triggered by protein phosphatase type 2A-mediated dephosphorylation of Maf1. Mol Cell 22: 623-632. (Pubitemid 43817597)
    • (2006) Molecular Cell , vol.22 , Issue.5 , pp. 623-632
    • Oficjalska-Pham, D.1    Harismendy, O.2    Smagowicz, W.J.3    Gonzalez De, P.A.4    Boguta, M.5    Sentenac, A.6    Lefebvre, O.7
  • 26
    • 54949143524 scopus 로고    scopus 로고
    • Maf1, a new player in the regulation of human RNA polymerase III transcription
    • Reina JH, Azzouz TN, Hernandez N. 2006. Maf1, a new player in the regulation of human RNA polymerase III transcription. PLoS ONE 1: e134.
    • (2006) PLoS ONE , vol.1
    • Reina, J.H.1    Azzouz, T.N.2    Hernandez, N.3
  • 28
    • 33644617485 scopus 로고    scopus 로고
    • Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions
    • Ripperger J, Schibler U. 2006. Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat Genet 38: 369-374.
    • (2006) Nat Genet , vol.38 , pp. 369-374
    • Ripperger, J.1    Schibler, U.2
  • 30
    • 33744515555 scopus 로고    scopus 로고
    • Dephosphorylation and Genome-Wide Association of Maf1 with Pol III-Transcribed Genes during Repression
    • DOI 10.1016/j.molcel.2006.04.009, PII S1097276506002541
    • Roberts DN, Wilson B, Huff JT, Stewart AJ, Cairns BR. 2006. Dephosphorylation and genome-wide association of Maf1with Pol III-transcribed genes during repression. Mol Cell 22: 633-644. (Pubitemid 43817598)
    • (2006) Molecular Cell , vol.22 , Issue.5 , pp. 633-644
    • Roberts, D.N.1    Wilson, B.2    Huff, J.T.3    Stewart, A.J.4    Cairns, B.R.5
  • 32
    • 0036923835 scopus 로고    scopus 로고
    • Maf1 is an essential mediator of diverse signals that repress RNA polymerase III transcription
    • DOI 10.1016/S1097-2765(02)00787-6
    • Upadhya R, Lee J, Willis IM. 2002. Maf1 is an essential mediator of diverse signals that repress RNA polymerase III transcription. Mol Cell 10: 1489-1494. (Pubitemid 36050888)
    • (2002) Molecular Cell , vol.10 , Issue.6 , pp. 1489-1494
    • Upadhya, R.1    Lee, J.2    Willis, I.M.3
  • 34
    • 2342538484 scopus 로고    scopus 로고
    • RNA polymerase III transcription and cancer
    • DOI 10.1038/sj.onc.1207547
    • White RJ. 2004. RNA polymerase III transcription and cancer. Oncogene 23: 3208-3216. (Pubitemid 38638832)
    • (2004) Oncogene , vol.23 , Issue.18 , pp. 3208-3216
    • White, R.J.1
  • 35
    • 33846659385 scopus 로고    scopus 로고
    • Integration of nutritional and stress signaling pathways by Maf1
    • DOI 10.1016/j.tibs.2006.12.001, PII S0968000406003264
    • Willis IM, Moir RD. 2007. Integration of nutritional and stress signaling pathways by Maf1. Trends Biochem Sci 32: 51-53. (Pubitemid 46199191)
    • (2007) Trends in Biochemical Sciences , vol.32 , Issue.2 , pp. 51-53
    • Willis, I.M.1    Moir, R.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.