Literature DB >> 28846090

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

M Ryan Corces1,2, Alexandro E Trevino1,3,4, Emily G Hamilton5, Peyton G Greenside3,6, Nicholas A Sinnott-Armstrong3, Sam Vesuna4, Ansuman T Satpathy1,7, Adam J Rubin2, Kathleen S Montine7, Beijing Wu3, Arwa Kathiria3, Seung Woo Cho1,2, Maxwell R Mumbach1,3, Ava C Carter1,2, Maya Kasowski1,7, Lisa A Orloff8, Viviana I Risca3, Anshul Kundaje3,9, Paul A Khavari2, Thomas J Montine7, William J Greenleaf1,3,10, Howard Y Chang1,2.   

Abstract

We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.

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Year:  2017        PMID： 28846090      PMCID： PMC5623106          DOI： 10.1038/nmeth.4396

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  23 in total

1.  The landscape of accessible chromatin in mammalian preimplantation embryos.

Authors:  Jingyi Wu; Bo Huang; He Chen; Qiangzong Yin; Yang Liu; Yunlong Xiang; Bingjie Zhang; Bofeng Liu; Qiujun Wang; Weikun Xia; Wenzhi Li; Yuanyuan Li; Jing Ma; Xu Peng; Hui Zheng; Jia Ming; Wenhao Zhang; Jing Zhang; Geng Tian; Feng Xu; Zai Chang; Jie Na; Xuerui Yang; Wei Xie
Journal:  Nature       Date:  2016-06-15       Impact factor: 49.962

2.  Distinct Gene Regulatory Pathways for Human Innate versus Adaptive Lymphoid Cells.

Authors:  Olivia I Koues; Patrick L Collins; Marina Cella; Michelle L Robinette; Sofia I Porter; Sarah C Pyfrom; Jacqueline E Payton; Marco Colonna; Eugene M Oltz
Journal:  Cell       Date:  2016-05-05       Impact factor: 41.582

3.  Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality.

Authors:  Han-Yu Shih; Giuseppe Sciumè; Yohei Mikami; Liying Guo; Hong-Wei Sun; Stephen R Brooks; Joseph F Urban; Fred P Davis; Yuka Kanno; John J O'Shea
Journal:  Cell       Date:  2016-05-05       Impact factor: 41.582

4.  A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63.

Authors:  Xiaomin Bao; Adam J Rubin; Kun Qu; Jiajing Zhang; Paul G Giresi; Howard Y Chang; Paul A Khavari
Journal:  Genome Biol       Date:  2015-12-18       Impact factor: 13.583

5.  Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data.

Authors:  Jason Piper; Markus C Elze; Pierre Cauchy; Peter N Cockerill; Constanze Bonifer; Sascha Ott
Journal:  Nucleic Acids Res       Date:  2013-09-25       Impact factor: 16.971

6.  The genetic regulatory signature of type 2 diabetes in human skeletal muscle.

Authors:  Laura J Scott; Michael R Erdos; Jeroen R Huyghe; Ryan P Welch; Andrew T Beck; Brooke N Wolford; Peter S Chines; John P Didion; Narisu Narisu; Heather M Stringham; D Leland Taylor; Anne U Jackson; Swarooparani Vadlamudi; Lori L Bonnycastle; Leena Kinnunen; Jouko Saramies; Jouko Sundvall; Ricardo D'Oliveira Albanus; Anna Kiseleva; John Hensley; Gregory E Crawford; Hui Jiang; Xiaoquan Wen; Richard M Watanabe; Timo A Lakka; Karen L Mohlke; Markku Laakso; Jaakko Tuomilehto; Heikki A Koistinen; Michael Boehnke; Francis S Collins; Stephen C J Parker
Journal:  Nat Commun       Date:  2016-06-29       Impact factor: 14.919

7.  Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

Authors:  Alisa Mo; Eran A Mukamel; Fred P Davis; Chongyuan Luo; Gilbert L Henry; Serge Picard; Mark A Urich; Joseph R Nery; Terrence J Sejnowski; Ryan Lister; Sean R Eddy; Joseph R Ecker; Jeremy Nathans
Journal:  Neuron       Date:  2015-06-17       Impact factor: 17.173

8.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

9.  Residual association at C9orf72 suggests an alternative amyotrophic lateral sclerosis-causing hexanucleotide repeat.

Authors:  Ashley R Jones; Ione Woollacott; Aleksey Shatunov; Johnathan Cooper-Knock; Vladimir Buchman; William Sproviero; Bradley Smith; Kirsten M Scott; Rubika Balendra; Olubunmi Abel; Peter McGuffin; Catherine M Ellis; Pamela J Shaw; Karen E Morrison; Anne Farmer; Cathryn M Lewis; P Nigel Leigh; Christopher E Shaw; John F Powell; Ammar Al-Chalabi
Journal:  Neurobiol Aging       Date:  2013-04-12       Impact factor: 4.673

10.  Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution.

Authors:  M Ryan Corces; Jason D Buenrostro; Beijing Wu; Peyton G Greenside; Steven M Chan; Julie L Koenig; Michael P Snyder; Jonathan K Pritchard; Anshul Kundaje; William J Greenleaf; Ravindra Majeti; Howard Y Chang
Journal:  Nat Genet       Date:  2016-08-15       Impact factor: 38.330
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  552 in total

1.  The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in mice.

Authors:  Hongbing Liu; Sylvia Hilliard; Elizabeth Kelly; Chao-Hui Chen; Zubaida Saifudeen; Samir S El-Dahr
Journal:  J Biol Chem       Date:  2020-06-18       Impact factor: 5.157

2.  Lens differentiation is characterized by stage-specific changes in chromatin accessibility correlating with differentiation state-specific gene expression.

Authors:  Joshua Disatham; Daniel Chauss; Rifah Gheyas; Lisa Brennan; David Blanco; Lauren Daley; A Sue Menko; Marc Kantorow
Journal:  Dev Biol       Date:  2019-05-25       Impact factor: 3.582

3.  CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis.

Authors:  Michael A Augello; Deli Liu; Lesa D Deonarine; Brian D Robinson; Dennis Huang; Suzan Stelloo; Mirjam Blattner; Ashley S Doane; Elissa W P Wong; Yu Chen; Mark A Rubin; Himisha Beltran; Olivier Elemento; Andries M Bergman; Wilbert Zwart; Andrea Sboner; Noah Dephoure; Christopher E Barbieri
Journal:  Cancer Cell       Date:  2019-03-28       Impact factor: 31.743

4.  Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells.

Authors:  Michael Delacher; Malte Simon; Lieke Sanderink; Agnes Hotz-Wagenblatt; Marina Wuttke; Kathrin Schambeck; Lisa Schmidleithner; Sebastian Bittner; Asmita Pant; Uwe Ritter; Thomas Hehlgans; Dania Riegel; Verena Schneider; Florian Kai Groeber-Becker; Andreas Eigenberger; Claudia Gebhard; Nicholas Strieder; Alexander Fischer; Michael Rehli; Petra Hoffmann; Matthias Edinger; Till Strowig; Jochen Huehn; Christian Schmidl; Jens M Werner; Lukas Prantl; Benedikt Brors; Charles D Imbusch; Markus Feuerer
Journal:  Immunity       Date:  2021-03-30       Impact factor: 31.745

5.  Initiation of Parental Genome Reprogramming in Fertilized Oocyte by Splicing Kinase SRPK1-Catalyzed Protamine Phosphorylation.

Authors:  Lan-Tao Gou; Do-Hwan Lim; Wubin Ma; Brandon E Aubol; Yajing Hao; Xin Wang; Jun Zhao; Zhengyu Liang; Changwei Shao; Xuan Zhang; Fan Meng; Hairi Li; Xiaorong Zhang; Ruiming Xu; Dangsheng Li; Michael G Rosenfeld; Pamela L Mellon; Joseph A Adams; Mo-Fang Liu; Xiang-Dong Fu
Journal:  Cell       Date:  2020-03-12       Impact factor: 41.582

6.  The cryptic unstable transcripts are associated with developmentally regulated gene expression in blood-stage Plasmodium falciparum.

Authors:  Shigang Yin; Yanting Fan; Xiaohui He; Guiying Wei; Yuhao Wen; Yuemeng Zhao; Mingli Shi; Jieqiong Wei; Huiling Chen; Jiping Han; Lubin Jiang; Qingfeng Zhang
Journal:  RNA Biol       Date:  2020-02-27       Impact factor: 4.652

7.  IL-15 Preconditioning Augments CAR T Cell Responses to Checkpoint Blockade for Improved Treatment of Solid Tumors.

Authors:  Lauren Giuffrida; Kevin Sek; Melissa A Henderson; Imran G House; Junyun Lai; Amanda X Y Chen; Kirsten L Todd; Emma V Petley; Sherly Mardiana; Izabela Todorovski; Emily Gruber; Madison J Kelly; Benjamin J Solomon; Stephin J Vervoort; Ricky W Johnstone; Ian A Parish; Paul J Neeson; Lev M Kats; Phillip K Darcy; Paul A Beavis
Journal:  Mol Ther       Date:  2020-07-21       Impact factor: 11.454

8.  Maintenance of CTCF- and Transcription Factor-Mediated Interactions from the Gametes to the Early Mouse Embryo.

Authors:  Yoon Hee Jung; Isaac Kremsky; Hannah B Gold; M Jordan Rowley; Kanchana Punyawai; Alyx Buonanotte; Xiaowen Lyu; Brianna J Bixler; Anthony W S Chan; Victor G Corces
Journal:  Mol Cell       Date:  2019-05-02       Impact factor: 17.970

9.  Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion.

Authors:  Ansuman T Satpathy; Jeffrey M Granja; Kathryn E Yost; Yanyan Qi; Francesca Meschi; Geoffrey P McDermott; Brett N Olsen; Maxwell R Mumbach; Sarah E Pierce; M Ryan Corces; Preyas Shah; Jason C Bell; Darisha Jhutty; Corey M Nemec; Jean Wang; Li Wang; Yifeng Yin; Paul G Giresi; Anne Lynn S Chang; Grace X Y Zheng; William J Greenleaf; Howard Y Chang
Journal:  Nat Biotechnol       Date:  2019-08-02       Impact factor: 54.908

10.  Mechanoresponsive stem cells acquire neural crest fate in jaw regeneration.

Authors:  Ryan C Ransom; Ava C Carter; Ankit Salhotra; Tripp Leavitt; Owen Marecic; Matthew P Murphy; Michael L Lopez; Yuning Wei; Clement D Marshall; Ethan Z Shen; Ruth Ellen Jones; Amnon Sharir; Ophir D Klein; Charles K F Chan; Derrick C Wan; Howard Y Chang; Michael T Longaker
Journal:  Nature       Date:  2018-10-24       Impact factor: 49.962
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