Mucosal viral infection elicits long-lived IgA responses via Type 1 follicular helper T cells

Original Data for the manuscript: Mucosal viral infection elicits long-lived IgA responses via Type 1 follicular helper T cells Kei Haniuda, Natalie M. Edner, Yuko Makita, Sandhya Appiah, Tania H. Watts, Gregory F. Wu, Thamotharampillai Dileepan and Jennifer L. Gommerman Cell 2025 https://doi.org/10.1016/j.cell.2025.07.022 bioRxiv 2025.01.27.635134; https://doi.org/10.1101/2025.01.27.635134 Please cite the journal publication when using any of this data. The raw data can be available from GSE287277 where barcodes, features and matrix gz files are stored. Original scRNA-seq data: Experiment 1 D7_1_barcodes.tsv.gz D7_1_features.tsv.gz D7_1_matrix.mtx.gz Experiment 2 D7_2_barcodes.tsv.gz D7_2_features.tsv.gz D7_2_matrix.mtx.gz Processed scRNA-seq data: CD4.cca2.rds --> Fully processed Seurat objects for CD4 T cell all CD4RV.cca2.rds --> Fully processed Seurat objects for RV T cell only (VP4 and VP6) Script: 1stRun.R --> R script for experiment 1 (use original data from Experiment 1) 2ndRun.R --> R script for experiment 2 (use original data from Experiment 2) Integration.all.R --> R script for integration of experiment 1 and 2 (for CD4 T cell all) Integration.RVonly.R --> R script for integration of experiment 1 and 2 (for RV T cell only) Package versions: Seurat: 5.0.1, patchwork 1.2.0, dplyr 1.1.4, ggplot2 3.4.4, sctransform 0.4.1, glmGamPoi 1.14.0, viridis 0.6.5, scCustomize 2.0.1, gprofiler2 0.2.2