Dataset for "Blood integrin and cytokine producing T cells are associated with stage and genetic risk score in age-related macular degeneration"

As a quality control measure, PBMC aliquots from internal controls were included in each experiment to monitor inter-experiment variability. Sample Breakdown: Controls (noAMD): 39 samples, labeled noAMD01 to noAMD39. Early / Intermediate AMD (eAMD): 21 samples, labeled eAMD01 to eAMD21.

Late AMD (lAMD): 38 samples, labeled lAMD01 to lAMD39 (lAMD13 was omitted, because something went wrong during FCM measurements) Internal Control Batch 1 (ICd): 6 samples, aliquots from control patient noAMD12, with sample IDs noAMD12_ICd01 to noAMD12_ICd06. Internal Control Batch 2 (ICr): 8 samples, aliquots from a buffy coat, with sample IDs ICr01 to ICr08. Data restrictions: Due to hospital data protection policies and privacy regulations, the data and metadata underlying this study are made available under restrictions.

Researchers may request access through the PI and data manager. Please fill out the request form or via de Contact Owner button (top right of this page). Information about the uploaded dataset files: A complete overview of all data files are described in README.

Below some of the important files are highlighted. Go the Files tab and click on Change view to Tree, which will reveal that the uploaded dataset consists of two parts: The FlowJo folder which contains all original files for the FlowJo analysis The R_project folder which contains the whole R project for data analysis. The FlowJo folder: Data_fcs folder containing 14 zip files with raw FCS files measured on 14 different experiment days.

WSP.zip in the Gating folder containing the Workspace (wsp) files for FlowJo analysis. GatingStrategy.zip in the Gating folder containing the gating tree strategy used in the wsp files for each panel. The R_project folder: FlowJoTables folder in the data folder containing frequency tables of cell populations for each panel (B, cDC, DCm, Tskew, T) extracted from FlowJo gating GRS table in the data folder containing GRS-52 for all samples, along with the allele scores for each of the 52 SNPs associated with AMD clinical data table in the metadata folder containing clinical information for all samples, including both patients and controls facs111_md table in the metadata folder containing clinical data for all samples measured in FCM, including patients, controls, and internal controls facs534_md table in the metadata folder containing file directories for all FCM-measured samples, along with some clinical information, including data for patients, controls, and internal controls paper_analysis.html is the data analysis script using the data and metadata resulting in all figures and tables for the paper (or see paper_analysis.Rmd) prep_stat table in the analysis folder containing combined clinical data, GRS data, and frequency tables of live cell populations for each panel (B, cDC, DCm, Tskew, T) extracted from FlowJo gating