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Items: 1 to 20 of 312

1.

Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology.

Wei G, Hu G, Cui K, Zhao K.

Methods Enzymol. 2012;513:297-313. doi: 10.1016/B978-0-12-391938-0.00013-6.

PMID:
22929775
2.

Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq.

Wal M, Pugh BF.

Methods Enzymol. 2012;513:233-50. doi: 10.1016/B978-0-12-391938-0.00010-0.

3.

Genome-wide mapping of nucleosomes in yeast using paired-end sequencing.

Cole HA, Howard BH, Clark DJ.

Methods Enzymol. 2012;513:145-68. doi: 10.1016/B978-0-12-391938-0.00006-9.

PMID:
22929768
4.
5.

Nucleosome-driven transcription factor binding and gene regulation.

Ballaré C, Castellano G, Gaveglia L, Althammer S, González-Vallinas J, Eyras E, Le Dily F, Zaurin R, Soronellas D, Vicent GP, Beato M.

Mol Cell. 2013 Jan 10;49(1):67-79. doi: 10.1016/j.molcel.2012.10.019.

6.

Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells.

Shin JH, Li RW, Gao Y, Baldwin R 6th, Li CJ.

Funct Integr Genomics. 2012 Mar;12(1):119-30. doi: 10.1007/s10142-012-0263-6.

PMID:
22249597
7.

Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.

Rye M, Sætrom P, Håndstad T, Drabløs F.

BMC Biol. 2011 Nov 24;9:80. doi: 10.1186/1741-7007-9-80.

8.

DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum.

Bunnik EM, Polishko A, Prudhomme J, Ponts N, Gill SS, Lonardi S, Le Roch KG.

BMC Genomics. 2014 May 8;15:347. doi: 10.1186/1471-2164-15-347.

9.

High-resolution genome-wide mapping of histone modifications.

Roh TY, Ngau WC, Cui K, Landsman D, Zhao K.

Nat Biotechnol. 2004 Aug;22(8):1013-6.

PMID:
15235610
10.

Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells.

de Dieuleveult M, Yen K, Hmitou I, Depaux A, Boussouar F, Bou Dargham D, Jounier S, Humbertclaude H, Ribierre F, Baulard C, Farrell NP, Park B, Keime C, Carrière L, Berlivet S, Gut M, Gut I, Werner M, Deleuze JF, Olaso R, Aude JC, Chantalat S, Pugh BF, Gérard M.

Nature. 2016 Feb 4;530(7588):113-6. doi: 10.1038/nature16505.

11.

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin.

Lund EG, Duband-Goulet I, Oldenburg A, Buendia B, Collas P.

Nucleus. 2015;6(1):30-9. doi: 10.4161/19491034.2014.990855.

12.

Mapping nucleosome positions using DNase-seq.

Zhong J, Luo K, Winter PS, Crawford GE, Iversen ES, Hartemink AJ.

Genome Res. 2016 Mar;26(3):351-64. doi: 10.1101/gr.195602.115.

13.

Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq.

Cui K, Zhao K.

Methods Mol Biol. 2012;833:413-9. doi: 10.1007/978-1-61779-477-3_24.

14.

Analysis of chromatin organization by deep sequencing technologies.

Platt JL, Kent NA, Harwood AJ, Kimmel AR.

Methods Mol Biol. 2013;983:173-83. doi: 10.1007/978-1-62703-302-2_9.

PMID:
23494307
15.

Asymmetric nucleosomes flank promoters in the budding yeast genome.

Ramachandran S, Zentner GE, Henikoff S.

Genome Res. 2015 Mar;25(3):381-90. doi: 10.1101/gr.182618.114.

16.

Analyzing the global chromatin structure of keratinocytes by MNase-seq.

Rizzo JM, Sinha S.

Methods Mol Biol. 2014;1195:49-59. doi: 10.1007/7651_2014_77.

PMID:
24676786
17.

A high-throughput ChIP-Seq for large-scale chromatin studies.

Chabbert CD, Adjalley SH, Klaus B, Fritsch ES, Gupta I, Pelechano V, Steinmetz LM.

Mol Syst Biol. 2015 Jan 12;11(1):777. doi: 10.15252/msb.20145776.

18.

Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.

Goh WS, Orlov Y, Li J, Clarke ND.

PLoS Comput Biol. 2010 Jan 22;6(1):e1000649. doi: 10.1371/journal.pcbi.1000649.

19.

ChIP on chip and ChIP-Seq assays: genome-wide analysis of transcription factor binding and histone modifications.

Pillai S, Chellappan SP.

Methods Mol Biol. 2015;1288:447-72. doi: 10.1007/978-1-4939-2474-5_26.

PMID:
25827896
20.

Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3.

Kraushaar DC, Jin W, Maunakea A, Abraham B, Ha M, Zhao K.

Genome Biol. 2013;14(10):R121. Erratum in: Genome Biol. 2016;17:21.

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