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