An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants.

Animals Cattle / genetics Chromatin Immunoprecipitation Sequencing High-Throughput Nucleotide Sequencing Sequence Analysis, DNA Chromatin / genetics Regulatory Sequences, Nucleic Acid

Journal

Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021

Informations de publication

Date de publication:
10 2023
Historique:
received: 01 04 2023
accepted: 19 09 2023
pmc-release: 01 04 2024
medline: 10 11 2023
pubmed: 27 9 2023
entrez: 26 9 2023
Statut: ppublish

Résumé

We report the generation of an organism-wide catalog of 976,813

Identifiants

DOI: 10.1101/gr.277947.123 PMID: 37751945 PMC: PMC10691486
pubmed: 37751945
pii: gr.277947.123
doi: 10.1101/gr.277947.123
pmc: PMC10691486
doi:

Substances chimiques

Chromatin 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1848-1864

Investigateurs

Mark Crowe (M)
Niamh McLoughlin (N)
Alan Fahey (A)
Elizabeth Matthews (E)
Andreia Santoro (A)
Colin Byrne (C)
Pauline Rudd (P)
Roisin O'Flaherty (R)
Sinead Hallinan (S)
Claire Wathes (C)
Zhangrui Cheng (Z)
Ali Fouladi (A)
Geoff Pollott (G)
Dirk Werling (D)
Beatriz Sanz Bernardo (BS)
Mazdak Salavati (M)
Laura Buggiotti (L)
Alistair Wylie (A)
Matt Bell (M)
Conrad Ferris (C)
Mieke Vaneetvelde (M)
Kristof Hermans (K)
Geert Opsomer (G)
Sander Moerman (S)
Jenne De Koster (J)
Hannes Bogaert (H)
Jan Vandepitte (J)
Leila Vandevelde (L)
Bonny Vanranst (B)
Johanna Hoglund (J)
Susanne Dahl (S)
Klaus Ingvartsen (K)
Martin Sørensen (M)
Leslie Foldager (L)
Soren Ostergaard (S)
Janne Rothmann (J)
Mogens Krogh (M)
Else Meyer (E)
Charlotte Gaillard (C)
Jehan Ettema (J)
Tine Rousing (T)
Federica Signorelli (F)
Francesco Napolitano (F)
Bianca Moioli (B)
Alessandra Crisa (A)
Luca Buttazzoni (L)
Jennifer McClure (J)
Daragh Matthews (D)
Francis Kearney (F)
Andrew Cromie (A)
Matt McClure (M)
Shujun Zhang (S)
Xing Chen (X)
Huanchun Chen (H)
Junlong Zhao (J)
Liguo Yang (L)
Guohua Hua (G)
Chen Tan (C)
Guiqiang Wang (G)
Michel Bonneau (M)
Andrea Pompozzi (A)
Armin Pearn (A)
Arnold Evertson (A)
Linda Kosten (L)
Anders Fogh (A)
Thomas Andersen (T)
Matthew Lucy (M)
Chris Elsik (C)
Gavin Conant (G)
Jerry Taylor (J)
Nicolas Gengler (N)
Michel Georges (M)
Frederic Colinet (F)
Marilou Ramos Pamplona (MR)
Hedi Hammami (H)
Catherine Bastin (C)
Haruko Takeda (H)
Aurelie Laine (A)
Lijing Tang (L)
Martin Schulze (M)
Cinzia Marchitelli (C)
Sergio Palma-Vera (S)

Informations de copyright

© 2023 Yuan et al.; Published by Cold Spring Harbor Laboratory Press.

Références

BMC Biol. 2019 Dec 30;17(1):108
pubmed: 31884969
Genome Res. 2002 Oct;12(10):1496-506
pubmed: 12368241
PLoS Comput Biol. 2010 May 06;6(5):e1000770
pubmed: 20463871
Nat Commun. 2020 Sep 17;11(1):4654
pubmed: 32943640
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Sci Rep. 2018 Jul 23;8(1):11096
pubmed: 30038226
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095
Nature. 2015 Feb 26;518(7540):502-506
pubmed: 25624100
Front Genet. 2018 Jul 30;9:281
pubmed: 30105049
Nat Genet. 2011 May;43(5):405-13
pubmed: 21516082
Genome Res. 2020 May;30(5):790-801
pubmed: 32424068
Nature. 2022 Feb;602(7895):101-105
pubmed: 35022609
Genetics. 2003 Jan;163(1):453-6
pubmed: 12586730
Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19398-19408
pubmed: 31501319
Epigenetics. 2021 Mar;16(3):300-312
pubmed: 32663104
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
PLoS Comput Biol. 2010 Dec 02;6(12):e1001025
pubmed: 21152010
Nature. 2020 Aug;584(7820):244-251
pubmed: 32728217
Nat Genet. 2016 Oct;48(10):1284-1287
pubmed: 27571263
Nature. 2003 Oct 23;425(6960):832-6
pubmed: 14574411
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Genome Biol. 2014;15(12):550
pubmed: 25516281
PLoS Biol. 2009 Dec;7(12):e1000256
pubmed: 20016685
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
Nat Commun. 2021 Mar 23;12(1):1821
pubmed: 33758196
BMC Genomics. 2021 Jan 6;22(1):14
pubmed: 33407093
Nature. 2020 Jul;583(7818):699-710
pubmed: 32728249
Nat Biotechnol. 2015 Mar;33(3):290-5
pubmed: 25690850
Nature. 2011 Oct 12;478(7370):476-82
pubmed: 21993624
J Dairy Sci. 2021 Mar;104(3):3596-3616
pubmed: 33455774
Genome Biol. 2010;11(12):R119
pubmed: 21143862
Cold Spring Harb Symp Quant Biol. 2004;69:477-83
pubmed: 16117683
Am J Hum Genet. 2015 Jul 2;97(1):139-52
pubmed: 26140449
BMC Genomics. 2022 Feb 15;23(1):130
pubmed: 35164677
Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4139-44
pubmed: 24591639
Genome Biol. 2010;11(10):R106
pubmed: 20979621
Cell. 2019 May 2;177(4):1022-1034.e6
pubmed: 31051098
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
PLoS Genet. 2021 Jul 21;17(7):e1009331
pubmed: 34288907
Genome Biol. 2008;9(9):R137
pubmed: 18798982
BMC Genomics. 2020 Aug 26;21(1):591
pubmed: 32847516
Genome Res. 2005 Jul;15(7):901-13
pubmed: 15965027
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Bioinformatics. 2011 Jun 15;27(12):1691-2
pubmed: 21493652
Nat Genet. 2022 Oct;54(10):1564-1571
pubmed: 36163278
BMC Genomics. 2020 Oct 7;21(1):698
pubmed: 33028202
Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):E3995-4004
pubmed: 27354521
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Bioinformatics. 2007 May 15;23(10):1294-6
pubmed: 17384015
Nature. 2016 Apr 14;532(7598):264-7
pubmed: 27075101
Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
pubmed: 12883005
Nat Methods. 2017 Oct;14(10):959-962
pubmed: 28846090
Genome Res. 2021 Nov;31(11):1994-2007
pubmed: 34417209
BMC Biol. 2019 Aug 16;17(1):68
pubmed: 31419979
Nat Commun. 2017 May 18;8:15452
pubmed: 28516912
BMC Genomics. 2018 Nov 3;19(1):793
pubmed: 30390624
Nat Commun. 2019 Nov 28;10(1):5436
pubmed: 31780650

Auteurs

Can Yuan (C)

Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.

Lijing Tang (L)

Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.

Thomas Lopdell (T)

Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand.
ORCID: 0000-0002-7684-4870

Vyacheslav A Petrov (VA)

Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.

Claire Oget-Ebrad (C)

Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.
ORCID: 0000-0003-1832-871X

Gabriel Costa Monteiro Moreira (GCM)

Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.

José Luis Gualdrón Duarte (JL)

Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.

Arnaud Sartelet (A)

Clinical Department of Ruminant, University of Liège, 4000 Liège, Belgium.

Zhangrui Cheng (Z)

Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom.

Mazdak Salavati (M)

Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom.

D Claire Wathes (DC)

Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom.

Mark A Crowe (MA)

School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland.

Wouter Coppieters (W)

GIGA Genomics platform, GIGA Institute, University of Liège, 4000 Liège, Belgium.

Mathew Littlejohn (M)

Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand.

Carole Charlier (C)

Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.

Tom Druet (T)

Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.
ORCID: 0000-0003-1637-1706

Michel Georges (M)

Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; michel.georges@uliege.be.

Haruko Takeda (H)

Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.
ORCID: 0000-0002-8455-6887

Articles similaires

Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.

Yue Zhang, Meifang Song, Deying Tang et al.
1.00
Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing

Evaluating the efficacy of telesurgery with dual console SSI Mantra Surgical Robotic System: experiment on animal model and clinical trials.

Sudhir Prem Srivastava, Vishwajyoti Pascual Srivastava, Avinesh Singh et al.
1.00
Robotic Surgical Procedures Animals Humans Telemedicine Models, Animal

Odour generalisation and detection dog training.

Lyn Caldicott, Thomas W Pike, Helen E Zulch et al.
1.00
Animals Odorants Dogs Generalization, Psychological Smell

FBXO22 inhibits colitis and colorectal carcinogenesis by regulating the degradation of the S2448-phosphorylated form of mTOR.

Minle Li, Xuan Chen, Pengfei Qu et al.
1.00
Animals TOR Serine-Threonine Kinases Colorectal Neoplasms Colitis Mice

Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › An organism-wide ATAC-seq peak catalog for the...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Artiodactyla › Ruminants › Bovins › An organism-wide ATAC-seq peak catalog for the...
questionsmedicales.fr › Techniques d'investigation › Techniques immunologiques › Immunoprécipitation › Immunoprécipitation de la chromatine › Séquençage après immunoprécipitation de la chromatine › An organism-wide ATAC-seq peak catalog for the...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › An organism-wide ATAC-seq peak catalog for the...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › An organism-wide ATAC-seq peak catalog for the...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › An organism-wide ATAC-seq peak catalog for the...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Séquences d'acides nucléiques régulatrices › An organism-wide ATAC-seq peak catalog for the...