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...
Main Authors: | , , , , , , |
---|---|
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 |
id |
doaj-94ed25d0d5a54e5785b11adb5093b187 |
---|---|
record_format |
Article |
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 |
work_keys_str_mv |
AT noudjoudattaf fb5pseqfacsbased5primeendsinglecellrnaseqforintegrativeanalysisoftranscriptomeandantigenreceptorrepertoireinbandtcells AT inakicerveramarzal fb5pseqfacsbased5primeendsinglecellrnaseqforintegrativeanalysisoftranscriptomeandantigenreceptorrepertoireinbandtcells AT chuangdong fb5pseqfacsbased5primeendsinglecellrnaseqforintegrativeanalysisoftranscriptomeandantigenreceptorrepertoireinbandtcells AT laurinegil fb5pseqfacsbased5primeendsinglecellrnaseqforintegrativeanalysisoftranscriptomeandantigenreceptorrepertoireinbandtcells AT amedeerenand fb5pseqfacsbased5primeendsinglecellrnaseqforintegrativeanalysisoftranscriptomeandantigenreceptorrepertoireinbandtcells AT lionelspinelli fb5pseqfacsbased5primeendsinglecellrnaseqforintegrativeanalysisoftranscriptomeandantigenreceptorrepertoireinbandtcells AT pierremilpied fb5pseqfacsbased5primeendsinglecellrnaseqforintegrativeanalysisoftranscriptomeandantigenreceptorrepertoireinbandtcells |
_version_ |
1724625505034960896 |