Literature DB >> 20150147

DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.

Lingyun Song1, Gregory E Crawford.   

Abstract

Entities:  

Mesh:

Substances:

Year:  2010        PMID: 20150147      PMCID: PMC3627383          DOI: 10.1101/pdb.prot5384

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


× No keyword cloud information.
  12 in total

1.  DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.

Authors:  Gregory E Crawford; Sean Davis; Peter C Scacheri; Gabriel Renaud; Mohamad J Halawi; Michael R Erdos; Roland Green; Paul S Meltzer; Tyra G Wolfsberg; Francis S Collins
Journal:  Nat Methods       Date:  2006-07       Impact factor: 28.547

2.  High-resolution mapping and characterization of open chromatin across the genome.

Authors:  Alan P Boyle; Sean Davis; Hennady P Shulha; Paul Meltzer; Elliott H Margulies; Zhiping Weng; Terrence S Furey; Gregory E Crawford
Journal:  Cell       Date:  2008-01-25       Impact factor: 41.582

Review 3.  Nuclease hypersensitive sites in chromatin.

Authors:  D S Gross; W T Garrard
Journal:  Annu Rev Biochem       Date:  1988       Impact factor: 23.643

4.  The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity.

Authors:  C Wu; Y C Wong; S C Elgin
Journal:  Cell       Date:  1979-04       Impact factor: 41.582

5.  Chromatin fine structure of active and repressed genes.

Authors:  A Levy; M Noll
Journal:  Nature       Date:  1981-01-15       Impact factor: 49.962

6.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

7.  Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).

Authors:  Yoichiro Shibata; Gregory E Crawford
Journal:  Methods Mol Biol       Date:  2009

8.  DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription.

Authors:  M A Keene; V Corces; K Lowenhaupt; S C Elgin
Journal:  Proc Natl Acad Sci U S A       Date:  1981-01       Impact factor: 11.205

9.  Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.

Authors:  Jay R Hesselberth; Xiaoyu Chen; Zhihong Zhang; Peter J Sabo; Richard Sandstrom; Alex P Reynolds; Robert E Thurman; Shane Neph; Michael S Kuehn; William S Noble; Stanley Fields; John A Stamatoyannopoulos
Journal:  Nat Methods       Date:  2009-03-22       Impact factor: 28.547

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

Authors:  Hualin Xi; Hennady P Shulha; Jane M Lin; Teresa R Vales; Yutao Fu; David M Bodine; Ronald D G McKay; Josh G Chenoweth; Paul J Tesar; Terrence S Furey; Bing Ren; Zhiping Weng; Gregory E Crawford
Journal:  PLoS Genet       Date:  2007-07-02       Impact factor: 5.917

View more
  250 in total

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

Authors:  Jeremy M Simon; Paul G Giresi; Ian J Davis; Jason D Lieb
Journal:  Nat Protoc       Date:  2012-01-19       Impact factor: 13.491

Review 2.  DNA-protein interactions: methods for detection and analysis.

Authors:  Bipasha Dey; Sameer Thukral; Shruti Krishnan; Mainak Chakrobarty; Sahil Gupta; Chanchal Manghani; Vibha Rani
Journal:  Mol Cell Biochem       Date:  2012-03-08       Impact factor: 3.396

3.  The decade of the epigenomes?

Authors:  Joost H A Martens; Hendrik G Stunnenberg; Colin Logie
Journal:  Genes Cancer       Date:  2011-06

4.  High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

Authors:  Alan P Boyle; Lingyun Song; Bum-Kyu Lee; Darin London; Damian Keefe; Ewan Birney; Vishwanath R Iyer; Gregory E Crawford; Terrence S Furey
Journal:  Genome Res       Date:  2010-11-24       Impact factor: 9.043

Review 5.  Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.

Authors:  Molly Megraw; Jason S Cumbie; Maria G Ivanchenko; Sergei A Filichkin
Journal:  Plant Cell       Date:  2016-02-11       Impact factor: 11.277

6.  Hormone-induced repression of genes requires BRG1-mediated H1.2 deposition at target promoters.

Authors:  Ana Silvina Nacht; Andy Pohl; Roser Zaurin; Daniel Soronellas; Javier Quilez; Priyanka Sharma; Roni H Wright; Miguel Beato; Guillermo P Vicent
Journal:  EMBO J       Date:  2016-07-07       Impact factor: 11.598

7.  Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.

Authors:  Michael L Stitzel; Praveen Sethupathy; Daniel S Pearson; Peter S Chines; Lingyun Song; Michael R Erdos; Ryan Welch; Stephen C J Parker; Alan P Boyle; Laura J Scott; Elliott H Margulies; Michael Boehnke; Terrence S Furey; Gregory E Crawford; Francis S Collins
Journal:  Cell Metab       Date:  2010-11-03       Impact factor: 27.287

Review 8.  ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.

Authors:  Terrence S Furey
Journal:  Nat Rev Genet       Date:  2012-10-23       Impact factor: 53.242

9.  TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets.

Authors:  Lori Glenwinkel; Di Wu; Gregory Minevich; Oliver Hobert
Journal:  Genetics       Date:  2014-02-20       Impact factor: 4.562

10.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.

Authors:  Jason D Buenrostro; Paul G Giresi; Lisa C Zaba; Howard Y Chang; William J Greenleaf
Journal:  Nat Methods       Date:  2013-10-06       Impact factor: 28.547

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.