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

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 rearrang...

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Main Authors: Noudjoud Attaf, Iñaki Cervera-Marzal, Chuang Dong, Laurine Gil, Amédée Renand, Lionel Spinelli, Pierre Milpied
Format: Article
Language:English
Published: Frontiers Media S.A. 2020-03-01
Series:Frontiers in Immunology
Subjects:
Online Access:https://www.frontiersin.org/article/10.3389/fimmu.2020.00216/full
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spelling doaj-94ed25d0d5a54e5785b11adb5093b1872020-11-25T03:18:51ZengFrontiers Media S.A.Frontiers in Immunology1664-32242020-03-011110.3389/fimmu.2020.00216504166FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T CellsNoudjoud Attaf0Iñaki Cervera-Marzal1Chuang Dong2Laurine Gil3Amédée Renand4Lionel Spinelli5Pierre Milpied6Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, FranceAix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, FranceAix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, FranceAix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, FranceCentre de Recherche en Transplantation et Immunologie UMR1064, INSERM Université de Nantes, Nantes, FranceAix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, FranceAix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, FranceSingle-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 CD4 T cells. We believe that our novel integrative scRNA-seq method will be a valuable option to study rare adaptive immune cell subsets in immunology research.https://www.frontiersin.org/article/10.3389/fimmu.2020.00216/fullsingle-cell RNA sequencingtranscriptomeantigen receptorB cellsT cells
collection DOAJ
language English
format Article
sources DOAJ
author Noudjoud Attaf
Iñaki Cervera-Marzal
Chuang Dong
Laurine Gil
Amédée Renand
Lionel Spinelli
Pierre Milpied
spellingShingle Noudjoud Attaf
Iñaki Cervera-Marzal
Chuang Dong
Laurine Gil
Amédée Renand
Lionel Spinelli
Pierre Milpied
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
single-cell RNA sequencing
transcriptome
antigen receptor
B cells
T cells
author_facet Noudjoud Attaf
Iñaki Cervera-Marzal
Chuang Dong
Laurine Gil
Amédée Renand
Lionel Spinelli
Pierre Milpied
author_sort Noudjoud Attaf
title 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
title_short 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
title_full 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
title_fullStr 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
title_full_unstemmed 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
title_sort 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
publisher Frontiers Media S.A.
series Frontiers in Immunology
issn 1664-3224
publishDate 2020-03-01
description 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 CD4 T cells. We believe that our novel integrative scRNA-seq method will be a valuable option to study rare adaptive immune cell subsets in immunology research.
topic single-cell RNA sequencing
transcriptome
antigen receptor
B cells
T cells
url https://www.frontiersin.org/article/10.3389/fimmu.2020.00216/full
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