Multi-organ CD45+ immune cell atlas

File Description MultiOrgan_MetaAtlas_total_level3_qc.rds: an rds file containing a Seurat object 114275 cells (RNA integrated assays, PCA and UMAP reductions and quality metrics) MultiOrgan_MetaAtlas_total_level3_qc.h5ad: an h5 file containing the single cell object as the above MultiOrgan_MetaAtlas_total_level3_qc_metadata.csv: a table containing the metadata for each cell Methodology 162 loom files were downloaded from the 12 different projects of the HCA consortium. In more detail, we focused on 14 different organs: prostate gland, eye, heart, skeletal muscle organ, blood, liver, spleen, brain, kidney, colon, esophagus, lung, thymus, and bone marrow. The files were transformed into Seurat objects with the function as.Seurat() from Seurat package in R. After incorporating metadata information, each object was screened for immune cells based on the expression of the CD45 immune marker. Specifically, cells were considered immune cells if they exhibited at least one read of the PTPRC - CD45 surface marker gene. Finally, the Seurat object was transformed into a .h5 object for Python users. Metadata All the files contain the following donor metadata variables: Tissue: Organ/tissues Project: Project of HCA Library_prep: single cell technology Sample_ID: assigned patient identifiers Tissue_part: specific location of the sampling Sex: the donor's sex Age: the donor's age percent.mt: Calculation of mitochondrial proportion percent.ribo: Calculation of ribosomal proportion annotation_level1: characterization of cells into the main immune compartments annotation_level2: focusing on each annotation_level1 category and performing in-depth characterization of the immune cells annotation_level3: focusing on the different subtypes of macrophages and the Tregs compartment The columns scDblFinder.class_rna, scDblFinder.score_rna, scDblFinder.weighted_rna, scDblFinder.cxds_score_rna are related to metrics for doublet detection using scDblFinder The columns S.Score, G2M.Score and Phase are related to cell cycling