Data and code for "PD-1 and ICOS are co-expressed in T follicular helper cells but define three stages of maturation of T follicular regulatory cells"

Data associated with the manuscript: "PD-1 and ICOS are co-expressed in T follicular helper cells but define three stages of maturation of T follicular regulatory cells" This dataset contains fluorescence values extracted from flow cytometry data processed in FlowJo and used for principal component analysis (PCA) of T follicular helper (Tfh) and T follicular regulatory (Tfr) cells from different human tonsils. Cells were gated as follows: TFH cells: lymphocytes/singlets/live CD4⁺FOXP3⁻CD25⁻CXCR5⁺ TFR cells: lymphocytes/singlets/live CD4⁺FOXP3⁺CXCR5⁺ The dataset includes samples from four different human tonsils, labeled as: t0, t1, t2, and t3. Available data files The uploaded ZIP file includes the following subfolders and files: 1. /raw_data: t0_TFH.csv, t1_TFH.csv, t2_TFH.csv, t3_TFH.csv: raw protein expression data for TFH cells (fluorescence values). t0_TFR.csv, t1_TFR.csv, t2_TFR.csv, t3_TFR.csv: raw protein expression data for TFR cells (fluorescence values). 2. /preprocessed_data: t0_tfh_pcs_subset.rds, t1_tfh_pcs_subset.rds, t2_tfh_pcs_subset.rds, t3_tfh_pcs_subset.rds: preprocessed TFH cell with data principal component scores. t0_tfr_pcs_subset.rds, t1_tfr_pcs_subset.rds, t2_tfr_pcs_subset.rds, t3_tfr_pcs_subset.rds: preprocessed TFR cell data with principal component scores. t0_combined_pcs.rds: preprocessed data for the combined PCA analysis of TFH and TFR cells from t0. 3. /documentation: tonsils_analysis_code.Rmd: R Markdown file with the code used for PCA analysis, visualization of PCA plots, and correlation heatmaps. tonsil_analysis_code.pdf: PDF version of the analysis code (rendered from the R Markdown file). tonsil_analysis_code.html: HTML version of the analysis code (rendered from the R Markdown file). Analysis and Code The R Markdown (RMD) file included in the repository provides: step-by-step code for PCA analysis visualization of PCA plots and correlation heatmaps shown in the manuscript