CyTOF_Mouse_Aging_Plasma

Investigating effects of aging and of pro-aging factors in blood on the immune system
Notes:
PLEASE READ ME - UPDATED APRIL 2024 >>Batch alignment for blood and spleen samples was performed using CytoNorm (Van Gassen et al., Mar 2020) for each tissue and experiment (e.g. adult/old and PBS/plasma-injected) separately. This batch alignment however induced noise in the staining of the brain samples and so the decision was made to work with the ‘raw’ data there instead. The processed FCS files were then uploaded into OMIQ data analysis software (https://www.omiq.ai) and data analysis was performed. First, normalization beads, cell debris, and cell doublets were removed from the data using Gaussian parameters, DNA staining, and bead intensity. Next, live cells that showed negative reactivity for viability marker Cell-ID™ Cisplatin-198Pt, negative reactivity for erythroid marker Ter119-154Sm, and dim-to-positive reactivity for CD45-89Y were selected. Parts with a stable flow were identified, selected, and used for further processing steps. >>All uploaded BLD and SPL .fcs files have been batch normalized, and the uploaded .fcs files from BLD, SPL, and CNS have been pre-gated following the specified strategy. >>Please note that for BLD and CNS of untreated 6-month-old and 20-month-old animals, there are discrepancies in barcode numbering between the mouse_coding_file_names.csv file and the .fcs sample names. Specifically, barcode number 1_c15 (#506) in the mouse_coding_file_names.csv is equivalent to 1_c18 in the .fcs samples; barcode number 1_c16 (#514) corresponds to 1_c19; and barcode number 2_c15 (#512) corresponds to 2_c18. These mismatches cannot be amended in the locked mouse_coding_file_names.csv file. The barcodes used during the experiment are those listed in the .fcs sample names.