Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis
Summary: 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 per...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723001806 |
| _version_ | 1797846387328548864 |
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| author | Jie Jia Yu Zhao Jian-Hua Wang Yi-Qun Kuang |
| author_facet | Jie Jia Yu Zhao Jian-Hua Wang Yi-Qun Kuang |
| author_sort | Jie Jia |
| collection | DOAJ |
| description | Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-09T17:54:07Z |
| format | Article |
| id | doaj.art-dda7eaaacd334906a76842aebda51386 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-09T17:54:07Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-dda7eaaacd334906a76842aebda513862023-04-15T05:54:56ZengElsevierSTAR Protocols2666-16672023-06-0142102222Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysisJie Jia0Yu Zhao1Jian-Hua Wang2Yi-Qun Kuang3NHC 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, ChinaNHC 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, ChinaGuangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; Corresponding authorNHC 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; Corresponding authorSummary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723001806BioinformaticsCell BiologyCell IsolationCell-based AssaysImmunologyMolecular Biology |
| spellingShingle | Jie Jia Yu Zhao Jian-Hua Wang Yi-Qun Kuang Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis STAR Protocols Bioinformatics Cell Biology Cell Isolation Cell-based Assays Immunology Molecular Biology |
| title | Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis |
| title_full | Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis |
| title_fullStr | Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis |
| title_full_unstemmed | Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis |
| title_short | Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis |
| title_sort | isolating peripheral blood mononuclear cells from hiv infected patients for single cell rna sequencing and integration analysis |
| topic | Bioinformatics Cell Biology Cell Isolation Cell-based Assays Immunology Molecular Biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723001806 |
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