FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells - Inserm - Institut national de la santé et de la recherche médicale Accéder directement au contenu
Article Dans Une Revue Frontiers in Immunology Année : 2020

FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells

Résumé

Single-cell RNA sequencing (scRNA-seq) allows the identification, characterization, and quantification of cell types in a tissue. When focused on B and T cells of the adaptive immune system, scRNA-seq carries the potential to track the clonal lineage of each analyzed cell through the unique rearranged sequence of its antigen receptor (BCR or TCR, respectively) and link it to the functional state inferred from transcriptome analysis. Here we introduce FB5P-seq, a FACS-based 5′-end scRNA-seq method for cost-effective, integrative analysis of transcriptome and paired BCR or TCR repertoire in phenotypically defined B and T cell subsets. We describe in detail the experimental workflow and provide a robust bioinformatics pipeline for computing gene count matrices and reconstructing repertoire sequences from FB5P-seq data. We further present two applications of FB5P-seq for the analysis of human tonsil B cell subsets and peripheral blood antigen-specific CD4T cells. We believe th at our novel integrative scRNA-seq method will be a valuable option to study rare adap tive immune cell subsets in immunology research.
Fichier principal
Vignette du fichier
fimmu-11-00216.pdf (1.48 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
Loading...

Dates et versions

inserm-02561110 , version 1 (03-05-2020)

Identifiants

Citer

Noudjoud Attaf, Inaki Cervera-Marzal, Chuang Dong, Laurine Gil, Amédée Renand, et al.. FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells. Frontiers in Immunology, 2020, 11, pp.216. ⟨10.3389/fimmu.2020.00216⟩. ⟨inserm-02561110⟩
93 Consultations
188 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More