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Items: 1 to 20 of 98

1.

The accessible chromatin landscape of the murine hippocampus at single-cell resolution.

Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Mulqueen RM, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC.

Genome Res. 2019 May;29(5):857-869. doi: 10.1101/gr.243725.118. Epub 2019 Apr 1.

PMID:
30936163
2.

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.

3.

The cis-regulatory dynamics of embryonic development at single-cell resolution.

Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM.

Nature. 2018 Mar 22;555(7697):538-542. doi: 10.1038/nature25981. Epub 2018 Mar 14.

4.

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J.

Cell. 2018 Aug 23;174(5):1309-1324.e18. doi: 10.1016/j.cell.2018.06.052. Epub 2018 Aug 2.

PMID:
30078704
5.

An ATAC-seq atlas of chromatin accessibility in mouse tissues.

Liu C, Wang M, Wei X, Wu L, Xu J, Dai X, Xia J, Cheng M, Yuan Y, Zhang P, Li J, Feng T, Chen A, Zhang W, Chen F, Shang Z, Zhang X, Peters BA, Liu L.

Sci Data. 2019 May 20;6(1):65. doi: 10.1038/s41597-019-0071-0.

6.

Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq.

Bajic M, Maher KA, Deal RB.

Methods Mol Biol. 2018;1675:183-201. doi: 10.1007/978-1-4939-7318-7_12.

7.

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.

Rubin AJ, Parker KR, Satpathy AT, Qi Y, Wu B, Ong AJ, Mumbach MR, Ji AL, Kim DS, Cho SW, Zarnegar BJ, Greenleaf WJ, Chang HY, Khavari PA.

Cell. 2019 Jan 10;176(1-2):361-376.e17. doi: 10.1016/j.cell.2018.11.022. Epub 2018 Dec 20.

PMID:
30580963
8.

Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks.

Starks RR, Biswas A, Jain A, Tuteja G.

Epigenetics Chromatin. 2019 Feb 22;12(1):16. doi: 10.1186/s13072-019-0260-2.

9.

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):233-244. doi: 10.1016/j.molmet.2016.01.002. eCollection 2016 Mar.

10.

Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone.

Ruf-Zamojski F, Fribourg M, Ge Y, Nair V, Pincas H, Zaslavsky E, Nudelman G, Tuminello SJ, Watanabe H, Turgeon JL, Sealfon SC.

Front Endocrinol (Lausanne). 2018 Feb 14;9:34. doi: 10.3389/fendo.2018.00034. eCollection 2018.

11.

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.

Ou J, Liu H, Yu J, Kelliher MA, Castilla LH, Lawson ND, Zhu LJ.

BMC Genomics. 2018 Mar 1;19(1):169. doi: 10.1186/s12864-018-4559-3.

12.

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
13.

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B.

Nat Neurosci. 2018 Mar;21(3):432-439. doi: 10.1038/s41593-018-0079-3. Epub 2018 Feb 12. Erratum in: Nat Neurosci. 2018 Mar 1;:.

14.

High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue.

Fujiwara S, Baek S, Varticovski L, Kim S, Hager GL.

Sci Rep. 2019 Jan 24;9(1):516. doi: 10.1038/s41598-018-36927-7.

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.

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.

17.

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.

18.

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
19.

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility.

Lareau CA, Duarte FM, Chew JG, Kartha VK, Burkett ZD, Kohlway AS, Pokholok D, Aryee MJ, Steemers FJ, Lebofsky R, Buenrostro JD.

Nat Biotechnol. 2019 Jun 24. doi: 10.1038/s41587-019-0147-6. [Epub ahead of print]

PMID:
31235917
20.

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

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