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ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes.
Rickner, Hannah D; Niu, Sheng-Yong; Cheng, Christine S.
Afiliação
  • Rickner HD; Department of Biology, Boston University.
  • Niu SY; Department of Biology, Boston University; Department of Computer Science and Engineering, University of California San Diego.
  • Cheng CS; Department of Biology, Boston University; Bioinformatics Program, Boston University; chcheng@bu.edu.
J Vis Exp ; (145)2019 03 22.
Article em En | MEDLINE | ID: mdl-30958473
ATAC-seq has become a widely used methodology in the study of epigenetics due to its rapid and simple approach to mapping genome-wide accessible chromatin. In this paper we present an improved ATAC-seq protocol that reduces contaminating mitochondrial DNA reads. While previous ATAC-seq protocols have struggled with an average of 50% contaminating mitochondrial DNA reads, the optimized lysis buffer introduced in this protocol reduces mitochondrial DNA contamination to an average of 3%. This improved ATAC-seq protocol allows for a near 50% reduction in the sequencing cost. We demonstrate how these high-quality ATAC-seq libraries can be prepared from activated CD4+ lymphocytes, providing step-by-step instructions from CD4+ lymphocyte isolation from whole blood through data analysis. This improved ATAC-seq protocol has been validated in a wide range of cell types and will be of immediate use to researchers studying chromatin accessibility.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: DNA Mitocondrial / Cromatina / Linfócitos T CD4-Positivos / Análise de Sequência de DNA / Transposases / Contaminação por DNA Limite: Humans Idioma: En Ano de publicação: 2019 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: DNA Mitocondrial / Cromatina / Linfócitos T CD4-Positivos / Análise de Sequência de DNA / Transposases / Contaminação por DNA Limite: Humans Idioma: En Ano de publicação: 2019 Tipo de documento: Article