TY  - JOUR
AU  - Braband, Kathrin Luise
AU  - Nedwed, Annekathrin Silvia
AU  - Helbich, Sara Salome
AU  - Simon, Malte
AU  - Beumer, Niklas
AU  - Brors, Benedikt
AU  - Marini, Federico
AU  - Delacher, Michael
TI  - Using single-cell chromatin accessibility sequencing to characterize CD4+ T cells from murine tissues.
JO  - Frontiers in immunology
VL  - 14
SN  - 1664-3224
CY  - Lausanne
PB  - Frontiers Media
M1  - DKFZ-2023-02221
SP  - 1232511
PY  - 2023
AB  - 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.
KW  - ArchR (Other)
KW  - Signac (Other)
KW  - T cell isolation (Other)
KW  - scATAC-seq (Other)
KW  - tissue digestion (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:37908367
C2  - pmc:PMC10613658
DO  - DOI:10.3389/fimmu.2023.1232511
UR  - https://inrepo02.dkfz.de/record/285097
ER  -