Dataset for: Altered follicular immunity in secondary lymphoid organs is associated with interferon hyperactivity in Down syndrome

Description This repository contains the flow cytometry and single-cell datasets generated for the study Altered follicular immunity in secondary lymphoid organs is associated with interferon hyperactivity in Down syndrome. Flow cytometry The flow cytometry dataset includes compensated Flow Cytometry Standard (FCS) files corresponding to four independent antibody panels designed to characterize immune cell populations from human palatine tonsils: T-cell panel (unstimulated) T-cell panel (stimulated) B-cell panel Myeloid-cell panel Data acquisition was performed using a BD LSRFortessa flow cytometer (BD Biosciences). The deposited FCS files correspond to exported gates containing viable cells after compensation and were used for all downstream analyses. Sample identifiers were anonymized prior to deposition. Single-cell multiomic data The single-cell dataset includes gene expression, paired T-cell receptor (TCR) sequencing, paired B-cell receptor (BCR) sequencing, and cell surface protein measurements generated from the same study cohort. Single-cell gene expression, paired TCR sequencing, and surface protein profiling were performed using the Chromium GEM-X Single Cell 5′ v3 Gene Expression with Feature Barcoding technology for Cell Surface Protein (10x Genomics), according to the manufacturer's instructions. Cell surface proteins were labeled using the TotalSeq™-C Human Universal Cocktail, V1.0 (BioLegend; Cat. No. 399905). The repository includes the Cell Ranger output files required for downstream analyses, including the filtered feature-barcode matrices (matrix.mtx.gz), feature annotation files (features.tsv.gz), barcode files (barcodes.tsv.gz), as well as the paired TCR and BCR V(D)J output files.