Cell type-specific weighting-factors for accurate virtual single-cell RNA-sequencing of diverse organs

Abstract

AbstractComputational deconvolution of transcriptome data of organs/tissues uncovers their structural and functional complexities at cellular resolution without performing single-cell RNA-sequencing experiments. However, the deconvolution of highly heterogenous diverse organs/tissues remains a challenge. Herein, we report “cell type-specific weighting-factors” that are essential for accurate deconvolution, but critically lacking in the existing methods. We computed such weighting-factors for 97 cell-types across 10 mouse organs and demonstrate their effective usage in the Bayesian framework to generate their virtual single-cell RNA-sequencing data, hence accurately estimating both cell-type ratios and the complete transcriptome of each cell-type in these organs. The method also efficiently detects the temporal changes of such cell type-profiles during organ pathogenesis in disease models. Furthermore, we present its potential utility for human organ/bulk-tissue deconvolution. Taken together, the weighting-factors reported herein and their computation for new cell-types and/or new species such as human are essential tools/resources for studying high-resolution biology and disease.