Literature DB >> 25834253

Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing.

Justin L Cotney, James P Noonan.   

Abstract

Entities:  

Year:  2015        PMID: 25834253      PMCID: PMC5956515          DOI: 10.1101/pdb.err087585

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


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  7 in total

1.  ChIP-Seq identification of weakly conserved heart enhancers.

Authors:  Matthew J Blow; David J McCulley; Zirong Li; Tao Zhang; Jennifer A Akiyama; Amy Holt; Ingrid Plajzer-Frick; Malak Shoukry; Crystal Wright; Feng Chen; Veena Afzal; James Bristow; Bing Ren; Brian L Black; Edward M Rubin; Axel Visel; Len A Pennacchio
Journal:  Nat Genet       Date:  2010-08-22       Impact factor: 38.330

2.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.

Authors:  Stephen A Bustin; Vladimir Benes; Jeremy A Garson; Jan Hellemans; Jim Huggett; Mikael Kubista; Reinhold Mueller; Tania Nolan; Michael W Pfaffl; Gregory L Shipley; Jo Vandesompele; Carl T Wittwer
Journal:  Clin Chem       Date:  2009-02-26       Impact factor: 8.327

3.  A map of the cis-regulatory sequences in the mouse genome.

Authors:  Yin Shen; Feng Yue; David F McCleary; Zhen Ye; Lee Edsall; Samantha Kuan; Ulrich Wagner; Jesse Dixon; Leonard Lee; Victor V Lobanenkov; Bing Ren
Journal:  Nature       Date:  2012-08-02       Impact factor: 49.962

4.  ChIP-seq accurately predicts tissue-specific activity of enhancers.

Authors:  Axel Visel; Matthew J Blow; Zirong Li; Tao Zhang; Jennifer A Akiyama; Amy Holt; Ingrid Plajzer-Frick; Malak Shoukry; Crystal Wright; Feng Chen; Veena Afzal; Bing Ren; Edward M Rubin; Len A Pennacchio
Journal:  Nature       Date:  2009-02-12       Impact factor: 49.962

5.  The evolution of lineage-specific regulatory activities in the human embryonic limb.

Authors:  Justin Cotney; Jing Leng; Jun Yin; Steven K Reilly; Laura E DeMare; Deena Emera; Albert E Ayoub; Pasko Rakic; James P Noonan
Journal:  Cell       Date:  2013-07-03       Impact factor: 41.582

6.  An expansive human regulatory lexicon encoded in transcription factor footprints.

Authors:  Shane Neph; Jeff Vierstra; Andrew B Stergachis; Alex P Reynolds; Eric Haugen; Benjamin Vernot; Robert E Thurman; Sam John; Richard Sandstrom; Audra K Johnson; Matthew T Maurano; Richard Humbert; Eric Rynes; Hao Wang; Shinny Vong; Kristen Lee; Daniel Bates; Morgan Diegel; Vaughn Roach; Douglas Dunn; Jun Neri; Anthony Schafer; R Scott Hansen; Tanya Kutyavin; Erika Giste; Molly Weaver; Theresa Canfield; Peter Sabo; Miaohua Zhang; Gayathri Balasundaram; Rachel Byron; Michael J MacCoss; Joshua M Akey; M A Bender; Mark Groudine; Rajinder Kaul; John A Stamatoyannopoulos
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

7.  The accessible chromatin landscape of the human genome.

Authors:  Robert E Thurman; Eric Rynes; Richard Humbert; Jeff Vierstra; Matthew T Maurano; Eric Haugen; Nathan C Sheffield; Andrew B Stergachis; Hao Wang; Benjamin Vernot; Kavita Garg; Sam John; Richard Sandstrom; Daniel Bates; Lisa Boatman; Theresa K Canfield; Morgan Diegel; Douglas Dunn; Abigail K Ebersol; Tristan Frum; Erika Giste; Audra K Johnson; Ericka M Johnson; Tanya Kutyavin; Bryan Lajoie; Bum-Kyu Lee; Kristen Lee; Darin London; Dimitra Lotakis; Shane Neph; Fidencio Neri; Eric D Nguyen; Hongzhu Qu; Alex P Reynolds; Vaughn Roach; Alexias Safi; Minerva E Sanchez; Amartya Sanyal; Anthony Shafer; Jeremy M Simon; Lingyun Song; Shinny Vong; Molly Weaver; Yongqi Yan; Zhancheng Zhang; Zhuzhu Zhang; Boris Lenhard; Muneesh Tewari; Michael O Dorschner; R Scott Hansen; Patrick A Navas; George Stamatoyannopoulos; Vishwanath R Iyer; Jason D Lieb; Shamil R Sunyaev; Joshua M Akey; Peter J Sabo; Rajinder Kaul; Terrence S Furey; Job Dekker; Gregory E Crawford; John A Stamatoyannopoulos
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

  7 in total
  7 in total

1.  A bipartite boundary element restricts UBE3A imprinting to mature neurons.

Authors:  Jack S Hsiao; Noelle D Germain; Andrea Wilderman; Christopher Stoddard; Luke A Wojenski; Geno J Villafano; Leighton Core; Justin Cotney; Stormy J Chamberlain
Journal:  Proc Natl Acad Sci U S A       Date:  2019-01-23       Impact factor: 11.205

2.  Marked Diversity of Unique Cortical Enhancers Enables Neuron-Specific Tools by Enhancer-Driven Gene Expression.

Authors:  Stefan Blankvoort; Menno P Witter; James Noonan; Justin Cotney; Cliff Kentros
Journal:  Curr Biol       Date:  2018-06-28       Impact factor: 10.834

3.  Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis.

Authors:  Jennifer VanOudenhove; Tara N Yankee; Andrea Wilderman; Justin Cotney
Journal:  Circ Res       Date:  2020-08-09       Impact factor: 17.367

4.  Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome.

Authors:  Emily V Dutrow; Deena Emera; Kristina Yim; Severin Uebbing; Acadia A Kocher; Martina Krenzer; Timothy Nottoli; Daniel B Burkhardt; Smita Krishnaswamy; Angeliki Louvi; James P Noonan
Journal:  Nat Commun       Date:  2022-01-13       Impact factor: 14.919

5.  A novel method for the normalization of ChIP-qPCR data.

Authors:  Elizabeth R Solomon; Kevin K Caldwell; Andrea M Allan
Journal:  MethodsX       Date:  2021-08-31

6.  SIRT6 transcriptionally regulates fatty acid transport by suppressing PPARγ.

Authors:  Danish Khan; Tarannum Ara; Venkatraman Ravi; Raksha Rajagopal; Himani Tandon; Jayadevan Parvathy; Edward A Gonzalez; Ninitha Asirvatham-Jeyaraj; Swati Krishna; Sneha Mishra; Sukanya Raghu; Arvind Singh Bhati; Ankit Kumar Tamta; Subhajit Dasgupta; Ullas Kolthur-Seetharam; Jean-Pierre Etchegaray; Raul Mostoslavsky; Prasanna Simha Mohan Rao; Narayanaswamy Srinivasan; Nagalingam Ravi Sundaresan
Journal:  Cell Rep       Date:  2021-06-01       Impact factor: 9.423

7.  Developmental arsenic exposure is associated with sex differences in the epigenetic regulation of stress genes in the adult mouse frontal cortex.

Authors:  Elizabeth R Solomon; Kevin K Caldwell; Andrea M Allan
Journal:  Toxicol Appl Pharmacol       Date:  2020-02-13       Impact factor: 4.219

  7 in total

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