Multiplexed single-cell RNA-sequencing of mouse thymic and splenic samples

Saran Pankaew; Clémence Grosjean; Julie Quessada; Marie Loosveld; Delphine Potier; Dominique Payet-Bornet; Mathis Nozais

doi:10.1016/j.xpro.2021.101041

Multiplexed single-cell RNA-sequencing of mouse thymic and splenic samples

STAR Protoc. 2021 Dec 20;3(1):101041. doi: 10.1016/j.xpro.2021.101041. Online ahead of print.

Authors

Saran Pankaew¹, Clémence Grosjean¹, Julie Quessada¹, Marie Loosveld², Delphine Potier¹, Dominique Payet-Bornet³, Mathis Nozais⁴

Affiliations

¹ Aix Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille Luminy (CIML), Parc scientifique de Luminy, Case 906, 13288 Marseille Cedex 9, France.
² Aix Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille Luminy (CIML), Parc scientifique de Luminy, Case 906, 13288 Marseille Cedex 9, France; APHM, Hôpital La Timone, Laboratoire d'Hématologie, Marseille, France.
³ Aix Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille Luminy (CIML), Parc scientifique de Luminy, Case 906, 13288 Marseille Cedex 9, France. Electronic address: payet@ciml.univ-mrs.fr.
⁴ Aix Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille Luminy (CIML), Parc scientifique de Luminy, Case 906, 13288 Marseille Cedex 9, France. Electronic address: nozais@ciml.univ-mrs.fr.

Abstract

Multiplexed single-cell RNA-sequencing (scRNA-seq) enables investigating several biological samples in one scRNA-seq experiment. Here, we use antibodies tagged with a hashtag oligonucleotide (Ab-HTO) to label each sample, and 10× Genomics technology to analyze single-cell gene expression. Advantages of sample multiplexing are to reduce the cost of scRNA-seq assay and to avoid batch effect. It may also facilitate cell-doublet removal and the merging of several scRNA-seq assays. Herein, we apply multiplexed scRNA-seq to investigate mouse thymocytes and splenic T lymphocytes development. For complete details on the use and execution of this protocol, please refer to Nozais et al. (2021).

Keywords: Antibody; Bioinformatics; Flow Cytometry/Mass Cytometry; Immunology; RNAseq; Sequence analysis; Sequencing; Single Cell.