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Items: 1 to 20 of 142

1.

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.

Genome Res. 2011 Oct;21(10):1757-67. doi: 10.1101/gr.121541.111. Epub 2011 Jul 12.

2.

Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.

Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RD, Chenoweth JG, Tesar PJ, Furey TS, Ren B, Weng Z, Crawford GE.

PLoS Genet. 2007 Aug;3(8):e136. Epub 2007 Jul 2.

3.

Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation.

Waki H, Nakamura M, Yamauchi T, Wakabayashi K, Yu J, Hirose-Yotsuya L, Take K, Sun W, Iwabu M, Okada-Iwabu M, Fujita T, Aoyama T, Tsutsumi S, Ueki K, Kodama T, Sakai J, Aburatani H, Kadowaki T.

PLoS Genet. 2011 Oct;7(10):e1002311. doi: 10.1371/journal.pgen.1002311. Epub 2011 Oct 20.

4.

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).

Giresi PG, Lieb JD.

Methods. 2009 Jul;48(3):233-9. doi: 10.1016/j.ymeth.2009.03.003. Epub 2009 Mar 18.

5.

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.

Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD.

Genome Res. 2007 Jun;17(6):877-85. Epub 2006 Dec 19.

6.

A map of open chromatin in human pancreatic islets.

Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D, Berney T, Montanya E, Mohlke KL, Lieb JD, Ferrer J.

Nat Genet. 2010 Mar;42(3):255-9. doi: 10.1038/ng.530. Epub 2010 Jan 31.

7.

Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) analysis uncovers broad changes in chromatin structure resulting from hexavalent chromium exposure.

Ovesen JL, Fan Y, Zhang X, Chen J, Medvedovic M, Xia Y, Puga A.

PLoS One. 2014 May 16;9(5):e97849. doi: 10.1371/journal.pone.0097849. eCollection 2014.

8.

Formaldehyde-assisted isolation of regulatory elements.

Nagy PL, Price DH.

Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):400-6. doi: 10.1002/wsbm.36. Review.

9.

The open chromatin landscape of Kaposi's sarcoma-associated herpesvirus.

Hilton IB, Simon JM, Lieb JD, Davis IJ, Damania B, Dittmer DP.

J Virol. 2013 Nov;87(21):11831-42. doi: 10.1128/JVI.01685-13. Epub 2013 Aug 28.

10.

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.

Simon JM, Giresi PG, Davis IJ, Lieb JD.

Nat Protoc. 2012 Jan 19;7(2):256-67. doi: 10.1038/nprot.2011.444. Erratum in: Nat Protoc. 2014 Feb;9(2):501-3.

11.

High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti.

Behura SK, Sarro J, Li P, Mysore K, Severson DW, Emrich SJ, Duman-Scheel M.

BMC Genomics. 2016 May 10;17:341. doi: 10.1186/s12864-016-2468-x.

12.

Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq).

Bianco S, Rodrigue S, Murphy BD, Gévry N.

Methods Mol Biol. 2015;1334:261-72. doi: 10.1007/978-1-4939-2877-4_17.

PMID:
26404156
13.

Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains.

Shu W, Chen H, Bo X, Wang S.

Nucleic Acids Res. 2011 Sep 1;39(17):7428-43. doi: 10.1093/nar/gkr443. Epub 2011 Jun 17.

14.

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.

15.

Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci.

Paul DS, Albers CA, Rendon A, Voss K, Stephens J; HaemGen Consortium, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH, Deloukas P.

Genome Res. 2013 Jul;23(7):1130-41. doi: 10.1101/gr.155127.113. Epub 2013 Apr 9.

16.

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.

Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS.

Genome Res. 2013 May;23(5):777-88. doi: 10.1101/gr.152140.112. Epub 2013 Mar 12.

17.

Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes.

Ackermann AM, Wang Z, Schug J, Naji A, Kaestner KH.

Mol Metab. 2016 Jan 11;5(3):233-44. doi: 10.1016/j.molmet.2016.01.002. eCollection 2016 Mar.

18.

Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells.

Hong CP, Choe MK, Roh TY.

Genomics Inform. 2012 Sep;10(3):145-52. doi: 10.5808/GI.2012.10.3.145. Epub 2012 Sep 28.

19.

Mapping accessible chromatin regions using Sono-Seq.

Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M.

Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14926-31. doi: 10.1073/pnas.0905443106. Epub 2009 Aug 18.

20.

Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators.

Sun J, Rockowitz S, Chauss D, Wang P, Kantorow M, Zheng D, Cvekl A.

Mol Vis. 2015 Aug 28;21:955-73. eCollection 2015.

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