As core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and their regulatory networks for understanding the biological mechanisms related to health and disease. However, a systematic and comprehensive single-cell transcriptional profile across multiple organs of a normal human adult is missing.
We perform single-cell transcriptomes of 84,363 cells derived from 15 tissue organs of one adult donor and generate an adult human cell atlas. The adult human cell atlas depicts 252 subtypes of cells, including major cell types such as T, B, myeloid, epithelial, and stromal cells, as well as novel COCH+ fibroblasts and FibSmo cells, each of which is distinguished by multiple marker genes and transcriptional profiles. These collectively contribute to the heterogeneity of major human organs. Moreover, T cell and B cell receptor repertoire comparisons and trajectory analyses reveal direct clonal sharing of T and B cells with various developmental states among different tissues. Furthermore, novel cell markers, transcription factors and ligand-receptor pairs are identified with potential functional regulations in maintaining the homeostasis of human cells among tissues.
The adult human cell atlas reveals the inter- and intra-organ heterogeneity of cell characteristics and provides a useful resource in uncovering key events during the development of human diseases in the context of the heterogeneity of cells and organs.
Please download the R package monocle V2.99 in the folder scRNA-AHCA/Data For Ploting/cole-trapnell-lab-monocle-release-2.99.tar.gz.
Please download and install the CellPhoneDB V2 at https://github.com/Teichlab/cellphonedb.
Please download and install the SCENIC at https://github.com/aertslab/SCENIC.
We developed an AHCA website for international users at http://research.gzsums.net:8888.
He, S., Wang, LH., Liu, Y. et al. Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs. Genome Biol 21, 294 (2020). https://doi.org/10.1186/s13059-020-02210-0
The files containing cell barcodes and corresponding annotation used in this study were uploaded to https://github.com/bei-lab/scRNA-AHCA/tree/master/Cell_barcode_and_corresponding_cell_types_of_AHCA folder. The non-filtered raw counts matrix were also uploaded to https://github.com/bei-lab/scRNA-AHCA/upload/master/No_filtered_Raw_counts_matrix folder. Please note that the cell barcodes of the raw count's matrix are not prefixed with corresponding tissue names, while it is easy to match cells in the raw counts matrix and annotation files manually.