GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals

Shiva Rezaei; Julia Uffenorde; Oliver Gimm; Mohammad Ali Hosseinpour Feizi; Stefan Miemczyk; Luiz Lehmann Coutinho; Per Jensen; Carlos Guerrero-Bosagna; Fábio Pértille

STAR Protocols (Mar 2022)

GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals

Shiva Rezaei,
Julia Uffenorde,
Oliver Gimm,
Mohammad Ali Hosseinpour Feizi,
Stefan Miemczyk,
Luiz Lehmann Coutinho,
Per Jensen,
Carlos Guerrero-Bosagna,
Fábio Pértille

Affiliations

Shiva Rezaei: Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran; Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
Julia Uffenorde: Department of Surgery and Department of Biomedical and Clinical Sciences (BKV), Linköping University, 581 83 Linköping, Sweden
Oliver Gimm: Department of Surgery and Department of Biomedical and Clinical Sciences (BKV), Linköping University, 581 83 Linköping, Sweden
Mohammad Ali Hosseinpour Feizi: Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran
Stefan Miemczyk: Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
Luiz Lehmann Coutinho: Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
Per Jensen: Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
Carlos Guerrero-Bosagna: Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden; Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden; Corresponding author
Fábio Pértille: Department of Surgery and Department of Biomedical and Clinical Sciences (BKV), Linköping University, 581 83 Linköping, Sweden; Avian Behavioral Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden; Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden; Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418-900, Brazil; Corresponding author

Journal volume & issue: Vol. 3, no. 1
p. 101202

Abstract

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Summary: The GBS-MeDIP protocol combines two previously described techniques, Genotype-by-Sequencing (GBS) and Methylated-DNA-Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of the barcoding of DNA samples performed in the GBS and the subsequent creation of DNA pools, then used as an input for the MeDIP. The GBS-MeDIP is particularly suitable to identify genetic and methylomic biomarkers when resources for whole genome interrogation are lacking.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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