Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species.

ABSTRACT: Analysis of gene expression in single cells allows for decomposition of cellular states as low-dimensional latent spaces. However, the interpretation and validation of these spaces remains a challenge. Here, we present scCoGAPS, which defines latent spaces from a source single-cell RNA-sequencing (scRNA-seq) dataset, and projectR, which evaluates these latent spaces in independent target datasets via transfer learning. Application of developing mouse retina to scRNA-Seq reveals intrinsic relationships across biological contexts and assays while avoiding batch effects and other technical features. We compare the dimensions learned in this source dataset to adult mouse retina, a time-course of human retinal development, select scRNA-seq datasets from developing brain, chromatin accessibility

SUBMITTER: Stein-O'Brien GL 

PROVIDER: S-EPMC6588402 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature