Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis

Jie Jia; Yu Zhao; Jian-Hua Wang; Yi-Qun Kuang

doi:10.1016/j.xpro.2023.102222

Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis

STAR Protoc. 2023 Apr 13;4(2):102222. doi: 10.1016/j.xpro.2023.102222. Online ahead of print.

Authors

Jie Jia¹, Yu Zhao¹, Jian-Hua Wang², Yi-Qun Kuang³

Affiliations

¹ NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University & Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming Medical University, Kunming, Yunnan 650032, China; Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China.
² Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China. Electronic address: wang_jianhua@gibh.ac.cn.
³ NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University & Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming Medical University, Kunming, Yunnan 650032, China; Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China. Electronic address: yq610433@hotmail.com.

Abstract

Single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) allows the dissection of transcriptional changes in immune cells with HIV infection. Here, we isolate PBMCs from HIV-infected individuals. After counting the cell number and verifying cell viability, we perform scRNA-seq for PBMCs on the 10× Genomics protocol and the Illumina NovaSeq 6000 sequencing platform. Furthermore, we analyze the function and cellular trajectories of B cell subsets and B cell receptor (BCR) repertoire after filtering raw sequences data and normalizing gene expression. For complete details on the use and execution of this protocol, please refer to Jia et al. (2022).¹.

Keywords: Bioinformatics; Cell Biology; Cell Isolation; Cell-based Assays; Immunology; Molecular Biology; RNAseq; Sequence Analysis; Single Cell.