Using single-cell chromatin accessibility sequencing to characterize CD4+ T cells from murine tissues

Frontiers in Immunology

Immunology

Benedikt Brors¹  Malte Simon²  Niklas Beumer³  Kathrin Luise Braband⁴  Sara Salome Helbich⁴  Michael Delacher⁴  Annekathrin Silvia Nedwed⁵  Federico Marini⁶ 

[1] Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany;National Center for Tumor Diseases (NCT), Heidelberg, Germany;German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany;Faculty of Biosciences, Heidelberg University, Heidelberg, Germany;Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany;Faculty of Biosciences, Heidelberg University, Heidelberg, Germany;Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany;DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany;Division of Personalized Medical Oncology (A420), German Cancer Research Center (DKFZ), Heidelberg, Germany;Department of Personalized Oncology, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany;Institute of Immunology, University Medical Center Mainz, Mainz, Germany;Research Center for Immunotherapy (FZI), University Medical Center Mainz, Mainz, Germany;Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany;Research Center for Immunotherapy (FZI), University Medical Center Mainz, Mainz, Germany;Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany;

关键词: scATAC-seq;    T cell isolation;    tissue digestion;    ArchR;    Signac;   

DOI  :  10.3389/fimmu.2023.1232511

 received in 2023-05-31, accepted in 2023-08-29,  发布年份 2023

来源: Frontiers

【 摘 要 】

The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a cutting-edge technology that enables researchers to assess genome-wide chromatin accessibility and to characterize cell type specific gene-regulatory programs. Recent technological progress allows for using this technology also on the single-cell level. In this article, we describe the whole value chain from the isolation of T cells from murine tissues to a complete bioinformatic analysis workflow. We start with methods for isolating scATAC-seq-ready CD4+ T cells from murine tissues such as visceral adipose tissue, skin, colon, and secondary lymphoid tissues such as the spleen. We describe the preparation of nuclei and quality control parameters during library preparation. Based on publicly available sequencing data that was generated using these protocols, we describe a step-by-step bioinformatic analysis pipeline for data pre-processing and downstream analysis. Our analysis workflow will follow the R-based bioinformatics framework ArchR, which is currently well established for scATAC-seq datasets. All in all, this work serves as a one-stop shop for generating and analyzing chromatin accessibility landscapes in T cells.

【 授权许可】

Unknown   
Copyright © 2023 Braband, Nedwed, Helbich, Simon, Beumer, Brors, Marini and Delacher