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Results: 1 to 20 of 81

1.

A detailed protocol for formaldehyde-assisted isolation of regulatory elements (FAIRE).

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

Curr Protoc Mol Biol. 2013;Chapter 21:Unit21.26. doi: 10.1002/0471142727.mb2126s102.

PMID:
23547014
[PubMed - indexed for MEDLINE]
2.

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.

PMID:
19303047
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
22262007
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
17179217
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
20046543
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Mapping open chromatin with formaldehyde-assisted isolation of regulatory elements.

Nammo T, Rodríguez-Seguí SA, Ferrer J.

Methods Mol Biol. 2011;791:287-96. doi: 10.1007/978-1-61779-316-5_21.

PMID:
21913087
[PubMed - indexed for MEDLINE]
7.

A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana.

Omidbakhshfard MA, Winck FV, Arvidsson S, Riaño-Pachón DM, Mueller-Roeber B.

J Integr Plant Biol. 2014 Jun;56(6):527-38. doi: 10.1111/jipb.12151. Epub 2014 Mar 16.

PMID:
24373132
[PubMed - in process]
8.

Isolation and analysis of DNA derived from nucleosome-free regions.

Murtha M, Wang Y, Basilico C, Dailey L.

Methods Mol Biol. 2013;977:35-51. doi: 10.1007/978-1-62703-284-1_4.

PMID:
23436352
[PubMed - indexed for MEDLINE]
9.

Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions.

Yaragatti M, Basilico C, Dailey L.

Genome Res. 2008 Jun;18(6):930-8. doi: 10.1101/gr.073460.107. Epub 2008 Apr 25.

PMID:
18441229
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
23166525
[PubMed]
Free PMC Article
11.

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.

PMID:
21750106
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
22028663
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast.

Wilhelm BT, Marguerat S, Aligianni S, Codlin S, Watt S, Bähler J.

Genome Biol. 2011 Aug 22;12(8):R82. doi: 10.1186/gb-2011-12-8-r82.

PMID:
21859475
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

High nucleosome occupancy is encoded at human regulatory sequences.

Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Field Y, Lieb JD, Widom J, Segal E, Hughes TR.

PLoS One. 2010 Feb 9;5(2):e9129. doi: 10.1371/journal.pone.0009129.

PMID:
20161746
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.

Wang YM, Zhou P, Wang LY, Li ZH, Zhang YN, Zhang YX.

PLoS One. 2012;7(8):e42414. doi: 10.1371/journal.pone.0042414. Epub 2012 Aug 10.

PMID:
22900019
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Isolation of intracellular protein--DNA complexes using HaloCHIP, an antibody-free alternative to chromatin immunoprecipitation.

Daniels DL, Urh M.

Methods Mol Biol. 2013;977:111-24. doi: 10.1007/978-1-62703-284-1_9.

PMID:
23436357
[PubMed - indexed for MEDLINE]
17.

Genetic landscape of open chromatin in yeast.

Lee K, Kim SC, Jung I, Kim K, Seo J, Lee HS, Bogu GK, Kim D, Lee S, Lee B, Choi JK.

PLoS Genet. 2013;9(2):e1003229. doi: 10.1371/journal.pgen.1003229. Epub 2013 Feb 7.

PMID:
23408895
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Alterations in chromatin accessibility and DNA methylation in clear cell renal cell carcinoma.

Buck MJ, Raaijmakers LM, Ramakrishnan S, Wang D, Valiyaparambil S, Liu S, Nowak NJ, Pili R.

Oncogene. 2013 Nov 4. doi: 10.1038/onc.2013.455. [Epub ahead of print]

PMID:
24186201
[PubMed - as supplied by publisher]
19.

Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals.

Halder K, Halder R, Chowdhury S.

Mol Biosyst. 2009 Dec;5(12):1703-12. doi: 10.1039/b905132e. Epub 2009 May 29.

PMID:
19587895
[PubMed - indexed for MEDLINE]
20.

Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites.

Shi B, Guo X, Wu T, Sheng S, Wang J, Skogerbø G, Zhu X, Chen R.

BMC Genomics. 2009 Feb 25;10:92. doi: 10.1186/1471-2164-10-92.

PMID:
19243610
[PubMed - indexed for MEDLINE]
Free PMC Article

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