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Volumn 6, Issue , 2017, Pages

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

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EID: 85022345215     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.23203     Document Type: Article
Times cited : (171)

References (39)
  • 1
    • 84929142779 scopus 로고    scopus 로고
    • Genomation: A toolkit to summarize, annotate and visualize genomic intervals
    • 25417204
    • Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D. 2015. Genomation: a toolkit to summarize, annotate and visualize genomic intervals. Bioinformatics 31:1127–1129. doi: 10.1093/bioinformatics/btu775, PMID: 25417204
    • (2015) Bioinformatics , vol.31 , pp. 1127-1129
    • Akalin, A.1    Franke, V.2    Vlahoviček, K.3    Mason, C.E.4    Schübeler, D.5
  • 3
    • 84949212255 scopus 로고    scopus 로고
    • ATAC-seq: A method for assaying chromatin accessibility Genome-Wide
    • 25559105
    • Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. 2015a. ATAC-seq: a method for assaying chromatin accessibility Genome-Wide. Current Protocols in Molecular Biology 109:21.29.1–21.29.9. doi: 10.1002/0471142727.mb2129s109, PMID: 25559105
    • (2015) Current Protocols in Molecular Biology , vol.109 , pp. 1-21
    • Buenrostro, J.D.1    Wu, B.2    Chang, H.Y.3    Greenleaf, W.J.4
  • 5
    • 84873351389 scopus 로고    scopus 로고
    • DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing
    • 23193179
    • Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. 2013. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Research 23:341–351. doi: 10.1101/gr.142067.112, PMID: 23193179
    • (2013) Genome Research , vol.23 , pp. 341-351
    • Chen, K.1    Xi, Y.2    Pan, X.3    Li, Z.4    Kaestner, K.5    Tyler, J.6    Dent, S.7    He, X.8    Li, W.9
  • 7
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • 22955616
    • ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74. doi: 10.1038/nature11247, PMID: 22955616
    • (2012) Nature , vol.489 , pp. 57-74
  • 9
    • 84924601067 scopus 로고    scopus 로고
    • Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics
    • 25732828
    • Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, Bock C. 2015. Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Reports 10:1386– 1397. doi: 10.1016/j.celrep.2015.02.001, PMID: 25732828
    • (2015) Cell Reports , vol.10
    • Farlik, M.1    Sheffield, N.C.2    Nuzzo, A.3    Datlinger, P.4    Schönegger, A.5    Klughammer, J.6    Bock, C.7
  • 13
    • 84870552401 scopus 로고    scopus 로고
    • Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
    • 22960375
    • Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. 2012. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Research 22:2497–2506. doi: 10.1101/gr.143008.112, PMID: 22960375
    • (2012) Genome Research , vol.22 , pp. 2497-2506
    • Kelly, T.K.1    Liu, Y.2    Lay, F.D.3    Liang, G.4    Berman, B.P.5    Jones, P.A.6
  • 15
    • 33847049022 scopus 로고    scopus 로고
    • Single-molecule and population probing of chromatin structure using DNA methyltransferases
    • 17309843
    • Kilgore JA, Hoose SA, Gustafson TL, Porter W, Kladde MP. 2007. Single-molecule and population probing of chromatin structure using DNA methyltransferases. Methods 41:320–332. doi: 10.1016/j.ymeth.2006.08.008, PMID: 17309843
    • (2007) Methods , vol.41 , pp. 320-332
    • Kilgore, J.A.1    Hoose, S.A.2    Gustafson, T.L.3    Porter, W.4    Kladde, M.P.5
  • 16
    • 84856498057 scopus 로고    scopus 로고
    • DNA methylome analysis using short bisulfite sequencing data
    • 22290186
    • Krueger F, Kreck B, Franke A, Andrews SR. 2012. DNA methylome analysis using short bisulfite sequencing data. Nature Methods 9:145–151. doi: 10.1038/nmeth.1828, PMID: 22290186
    • (2012) Nature Methods , vol.9 , pp. 145-151
    • Krueger, F.1    Kreck, B.2    Franke, A.3    Andrews, S.R.4
  • 17
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with bowtie 2
    • 22388286
    • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with bowtie 2. Nature Methods 9:357–359. doi: 10.1038/nmeth.1923, PMID: 22388286
    • (2012) Nature Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 18
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/Map format and SAMtools
    • 19505943
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. doi: 10.1093/bioinformatics/btp352, PMID: 19505943
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 20
    • 84938401651 scopus 로고    scopus 로고
    • Taking stock of regulatory variation
    • 27135686
    • Maurano MT, Stamatoyannopoulos JA. 2015. Taking stock of regulatory variation. Cell Systems 1:18–21. doi: 10. 1016/j.cels.2015.07.011, PMID: 27135686
    • (2015) Cell Systems , vol.1 , pp. 18-21
    • Maurano, M.T.1    Stamatoyannopoulos, J.A.2
  • 21
    • 75949101193 scopus 로고    scopus 로고
    • Methylation-sensitive single-molecule analysis of chromatin structure
    • Chapter 21:Unit 21.17.1–21.1716, 20069538
    • Miranda TB, Kelly TK, Bouazoune K, Jones PA. 2010. Methylation-sensitive single-molecule analysis of chromatin structure. Current Protocols in Molecular Biology Chapter 21:Unit 21.17.1–21.1716. doi: 10.1002/0471142727.mb2117s89, PMID: 20069538
    • (2010) Current Protocols in Molecular Biology
    • Miranda, T.B.1    Kelly, T.K.2    Bouazoune, K.3    Jones, P.A.4
  • 24
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • 20110278
    • Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. doi: 10.1093/bioinformatics/btq033, PMID: 20110278
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 27
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic regulation of nucleosome positioning in the human genome
    • 1832 9373
    • Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887–898. doi: 10.1016/j.cell.2008.02.022, PMID: 1832 9373
    • (2008) Cell , vol.132 , pp. 887-898
    • Schones, D.E.1    Cui, K.2    Cuddapah, S.3    Roh, T.Y.4    Barski, A.5    Wang, Z.6    Wei, G.7    Zhao, K.8
  • 28
    • 84922621952 scopus 로고    scopus 로고
    • Function and information content of DNA methylation
    • 25592537
    • Schübeler D. 2015. Function and information content of DNA methylation. Nature 517:321–326. doi: 10.1038/nature14192, PMID: 25592537
    • (2015) Nature , vol.517 , pp. 321-326
    • Schübeler, D.1
  • 30
    • 84902596852 scopus 로고    scopus 로고
    • Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity
    • 24889621
    • Small EC, Xi L, Wang JP, Widom J, Licht JD. 2014. Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity. PNAS 111:E2462–E2471. doi: 10.1073/pnas.1400517111, PMID: 24889621
    • (2014) PNAS , vol.111 , pp. E2462-E2471
    • Small, E.C.1    Xi, L.2    Wang, J.P.3    Widom, J.4    Licht, J.D.5
  • 33
    • 84907196865 scopus 로고    scopus 로고
    • Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in Cancer
    • 24916973
    • Taberlay PC, Statham AL, Kelly TK, Clark SJ, Jones PA. 2014. Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in Cancer. Genome Research 24:1421–1432. doi: 10.1101/gr.163485.113, PMID: 24916973
    • (2014) Genome Research , vol.24 , pp. 1421-1432
    • Taberlay, P.C.1    Statham, A.L.2    Kelly, T.K.3    Clark, S.J.4    Jones, P.A.5
  • 36
    • 79959557189 scopus 로고    scopus 로고
    • Determinants of nucleosome organization in primary human cells
    • 21602827
    • Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. 2011. Determinants of nucleosome organization in primary human cells. Nature 474:516–520. doi: 10.1038/nature10002, PMID: 21602827
    • (2011) Nature , vol.474 , pp. 516-520
    • Valouev, A.1    Johnson, S.M.2    Boyd, S.D.3    Smith, C.L.4    Fire, A.Z.5    Sidow, A.6
  • 38
    • 84909944591 scopus 로고    scopus 로고
    • New York, Springer Science & Business Media
    • Wickham H. 2009. Ggplot2. New York, Springer Science & Business Media.
    • (2009) Ggplot2
    • Wickham, H.1


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