Literature DB >> 20147195

Native chromatin preparation and Illumina/Solexa library construction.

Suresh Cuddapah1, Artem Barski, Kairong Cui, Dustin E Schones, Zhibin Wang, Gang Wei, Keji Zhao.   

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Year:  2009        PMID： 20147195      PMCID： PMC3541822          DOI： 10.1101/pdb.prot5237

Source DB:  PubMed          Journal:  Cold Spring Harb Protoc        ISSN： 1559-6095


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  10 in total

1.  High-resolution profiling of histone methylations in the human genome.

Authors:  Artem Barski; Suresh Cuddapah; Kairong Cui; Tae-Young Roh; Dustin E Schones; Zhibin Wang; Gang Wei; Iouri Chepelev; Keji Zhao
Journal:  Cell       Date:  2007-05-18       Impact factor: 41.582

Review 2.  Genome-wide approaches to studying chromatin modifications.

Authors:  Dustin E Schones; Keji Zhao
Journal:  Nat Rev Genet       Date:  2008-03       Impact factor: 53.242

3.  Combinatorial patterns of histone acetylations and methylations in the human genome.

Authors:  Zhibin Wang; Chongzhi Zang; Jeffrey A Rosenfeld; Dustin E Schones; Artem Barski; Suresh Cuddapah; Kairong Cui; Tae-Young Roh; Weiqun Peng; Michael Q Zhang; Keji Zhao
Journal:  Nat Genet       Date:  2008-06-15       Impact factor: 38.330

4.  The transcriptional landscape of the yeast genome defined by RNA sequencing.

Authors:  Ugrappa Nagalakshmi; Zhong Wang; Karl Waern; Chong Shou; Debasish Raha; Mark Gerstein; Michael Snyder
Journal:  Science       Date:  2008-05-01       Impact factor: 47.728

5.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

6.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Authors:  Gordon Robertson; Martin Hirst; Matthew Bainbridge; Misha Bilenky; Yongjun Zhao; Thomas Zeng; Ghia Euskirchen; Bridget Bernier; Richard Varhol; Allen Delaney; Nina Thiessen; Obi L Griffith; Ann He; Marco Marra; Michael Snyder; Steven Jones
Journal:  Nat Methods       Date:  2007-06-11       Impact factor: 28.547

7.  Dynamic regulation of nucleosome positioning in the human genome.

Authors:  Dustin E Schones; Kairong Cui; Suresh Cuddapah; Tae-Young Roh; Artem Barski; Zhibin Wang; Gang Wei; Keji Zhao
Journal:  Cell       Date:  2008-03-07       Impact factor: 41.582

8.  Genome-wide mapping of in vivo protein-DNA interactions.

Authors:  David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal:  Science       Date:  2007-05-31       Impact factor: 47.728

9.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

Authors:  Tarjei S Mikkelsen; Manching Ku; David B Jaffe; Biju Issac; Erez Lieberman; Georgia Giannoukos; Pablo Alvarez; William Brockman; Tae-Kyung Kim; Richard P Koche; William Lee; Eric Mendenhall; Aisling O'Donovan; Aviva Presser; Carsten Russ; Xiaohui Xie; Alexander Meissner; Marius Wernig; Rudolf Jaenisch; Chad Nusbaum; Eric S Lander; Bradley E Bernstein
Journal:  Nature       Date:  2007-07-01       Impact factor: 49.962

10.  Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

Authors:  Shawn J Cokus; Suhua Feng; Xiaoyu Zhang; Zugen Chen; Barry Merriman; Christian D Haudenschild; Sriharsa Pradhan; Stanley F Nelson; Matteo Pellegrini; Steven E Jacobsen
Journal:  Nature       Date:  2008-02-17       Impact factor: 49.962
  10 in total
  16 in total

1.  Comprehensive transcriptional profiling of NaHCO3-stressed Tamarix hispida roots reveals networks of responsive genes.

Authors:  Chao Wang; Caiqiu Gao; Liuqiang Wang; Lei Zheng; Chuanping Yang; Yucheng Wang
Journal:  Plant Mol Biol       Date:  2013-09-11       Impact factor: 4.076

2.  The transcription factor Pax6 regulates survival of dopaminergic olfactory bulb neurons via crystallin αA.

Authors:  Jovica Ninkovic; Luisa Pinto; Stefania Petricca; Alexandra Lepier; Jian Sun; Michael A Rieger; Timm Schroeder; Ales Cvekl; Jack Favor; Magdalena Götz
Journal:  Neuron       Date:  2010-11-18       Impact factor: 17.173

3.  Chromatin poises miRNA- and protein-coding genes for expression.

Authors:  Artem Barski; Raja Jothi; Suresh Cuddapah; Kairong Cui; Tae-Young Roh; Dustin E Schones; Keji Zhao
Journal:  Genome Res       Date:  2009-08-27       Impact factor: 9.043

4.  Microbiota-sensitive epigenetic signature predicts inflammation in Crohn's disease.

Authors:  Daniel Kelly; Michael Kotliar; Vivienne Woo; Sajjeev Jagannathan; Jordan Whitt; Jessica Moncivaiz; Bruce J Aronow; Marla C Dubinsky; Jeffrey S Hyams; James F Markowitz; Robert N Baldassano; Michael C Stephens; Thomas D Walters; Subra Kugathasan; Yael Haberman; Nambirajan Sundaram; Michael J Rosen; Michael Helmrath; Rebekah Karns; Artem Barski; Lee A Denson; Theresa Alenghat
Journal:  JCI Insight       Date:  2018-09-20

Review 5.  Epigenome mapping in normal and disease States.

Authors:  Alika K Maunakea; Iouri Chepelev; Keji Zhao
Journal:  Circ Res       Date:  2010-08-06       Impact factor: 17.367

Review 6.  Unraveling the 3D genome: genomics tools for multiscale exploration.

Authors:  Viviana I Risca; William J Greenleaf
Journal:  Trends Genet       Date:  2015-04-14       Impact factor: 11.639

7.  Long-distance regulation of fetal V(δ) gene segment TRDV4 by the Tcrd enhancer.

Authors:  Bingtao Hao; Michael S Krangel
Journal:  J Immunol       Date:  2011-07-22       Impact factor: 5.422

8.  IL-1β enhances inflammatory TH2 differentiation.

Authors:  Stephan M Caucheteux; Jane Hu-Li; Liying Guo; Nisan Bhattacharyya; Michelle Crank; Michael T Collins; William E Paul
Journal:  J Allergy Clin Immunol       Date:  2016-04-19       Impact factor: 10.793

9.  Genetic code expansion in stable cell lines enables encoded chromatin modification.

Authors:  Simon J Elsässer; Russell J Ernst; Olivia S Walker; Jason W Chin
Journal:  Nat Methods       Date:  2016-01-04       Impact factor: 28.547

10.  ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder.

Authors:  Leelavati Narlikar; Raja Jothi
Journal:  Methods Mol Biol       Date:  2012
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