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Items: 1 to 20 of 104

1.

The chromatin accessibility landscape of primary human cancers.

Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network, Greenleaf WJ, Chang HY.

Science. 2018 Oct 26;362(6413). pii: eaav1898. doi: 10.1126/science.aav1898.

2.

The landscape of accessible chromatin in mammalian preimplantation embryos.

Wu J, Huang B, Chen H, Yin Q, Liu Y, Xiang Y, Zhang B, Liu B, Wang Q, Xia W, Li W, Li Y, Ma J, Peng X, Zheng H, Ming J, Zhang W, Zhang J, Tian G, Xu F, Chang Z, Na J, Yang X, Xie W.

Nature. 2016 Jun 30;534(7609):652-7. Epub 2016 Jun 15.

PMID:
27309802
3.

Genetic regulatory signatures underlying islet gene expression and type 2 diabetes.

Varshney A, Scott LJ, Welch RP, Erdos MR, Chines PS, Narisu N, Albanus RD, Orchard P, Wolford BN, Kursawe R, Vadlamudi S, Cannon ME, Didion JP, Hensley J, Kirilusha A; NISC Comparative Sequencing Program, Bonnycastle LL, Taylor DL, Watanabe R, Mohlke KL, Boehnke M, Collins FS, Parker SC, Stitzel ML.

Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2301-2306. doi: 10.1073/pnas.1621192114. Epub 2017 Feb 13.

4.

Single-cell chromatin accessibility reveals principles of regulatory variation.

Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ.

Nature. 2015 Jul 23;523(7561):486-90. doi: 10.1038/nature14590. Epub 2015 Jun 17.

5.

The accessible chromatin landscape of the human genome.

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232.

6.

Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling.

Shashikant T, Khor JM, Ettensohn CA.

BMC Genomics. 2018 Mar 20;19(1):206. doi: 10.1186/s12864-018-4542-z.

7.

Assay for Transposase-Accessible Chromatin Using Sequencing (ATAC-seq) Data Analysis.

Miskimen KL, Chan ER, Haines JL.

Curr Protoc Hum Genet. 2017 Jan 11;92:20.4.1-20.4.13. doi: 10.1002/cphg.32.

PMID:
28075484
8.

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes.

Lu Z, Hofmeister BT, Vollmers C, DuBois RM, Schmitz RJ.

Nucleic Acids Res. 2017 Apr 7;45(6):e41. doi: 10.1093/nar/gkw1179.

9.

ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.

Buenrostro JD, Wu B, Chang HY, Greenleaf WJ.

Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-9. doi: 10.1002/0471142727.mb2129s109.

10.

Chromatin analysis in human early development reveals epigenetic transition during ZGA.

Wu J, Xu J, Liu B, Yao G, Wang P, Lin Z, Huang B, Wang X, Li T, Shi S, Zhang N, Duan F, Ming J, Zhang X, Niu W, Song W, Jin H, Guo Y, Dai S, Hu L, Fang L, Wang Q, Li Y, Li W, Na J, Xie W, Sun Y.

Nature. 2018 May;557(7704):256-260. doi: 10.1038/s41586-018-0080-8. Epub 2018 May 2. Erratum in: Nature. 2018 Aug;560(7718):E27.

PMID:
29720659
11.

On the identification of potential regulatory variants within genome wide association candidate SNP sets.

Chen CY, Chang IS, Hsiung CA, Wasserman WW.

BMC Med Genomics. 2014 Jun 11;7:34. doi: 10.1186/1755-8794-7-34.

12.

Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq.

Tannenbaum M, Sarusi-Portuguez A, Krispil R, Schwartz M, Loza O, Benichou JIC, Mosquna A, Hakim O.

Plant Methods. 2018 Dec 20;14:113. doi: 10.1186/s13007-018-0381-9. eCollection 2018.

13.

Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci.

Fullard JF, Giambartolomei C, Hauberg ME, Xu K, Voloudakis G, Shao Z, Bare C, Dudley JT, Mattheisen M, Robakis NK, Haroutunian V, Roussos P.

Hum Mol Genet. 2017 May 15;26(10):1942-1951. doi: 10.1093/hmg/ddx103.

14.

Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq.

Ho MCW, Quintero-Cadena P, Sternberg PW.

Genome Res. 2017 Dec;27(12):2108-2119. doi: 10.1101/gr.223735.117. Epub 2017 Oct 26.

15.

An atlas of chromatin accessibility in the adult human brain.

Fullard JF, Hauberg ME, Bendl J, Egervari G, Cirnaru MD, Reach SM, Motl J, Ehrlich ME, Hurd YL, Roussos P.

Genome Res. 2018 Aug;28(8):1243-1252. doi: 10.1101/gr.232488.117. Epub 2018 Jun 26.

16.

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.

Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY.

Nat Methods. 2016 Dec;13(12):1013-1020. doi: 10.1038/nmeth.4031. Epub 2016 Oct 17.

17.

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq.

Grbesa I, Tannenbaum M, Sarusi-Portuguez A, Schwartz M, Hakim O.

J Vis Exp. 2017 Nov 13;(129). doi: 10.3791/56313.

PMID:
29155775
18.

Assay for Transposase Accessible Chromatin (ATAC-Seq) to Chart the Open Chromatin Landscape of Human Pancreatic Islets.

Raurell-Vila H, Ramos-Rodríguez M, Pasquali L.

Methods Mol Biol. 2018;1766:197-208. doi: 10.1007/978-1-4939-7768-0_11.

PMID:
29605854
19.

Genome-wide analysis of chromatin accessibility using ATAC-seq.

Shashikant T, Ettensohn CA.

Methods Cell Biol. 2019;151:219-235. doi: 10.1016/bs.mcb.2018.11.002. Epub 2018 Dec 21.

PMID:
30948010
20.

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.

Chen H, Li C, Peng X, Zhou Z, Weinstein JN; Cancer Genome Atlas Research Network, Liang H.

Cell. 2018 Apr 5;173(2):386-399.e12. doi: 10.1016/j.cell.2018.03.027.

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