Understanding the transcriptional response to ER stress in Chinese hamster ovary cells using multiplexed single cell RNA-seq

Single cell RNA-seq (scRNA-seq) has recently been shown to provide a powerful method for the analysis of transcriptional heterogeneity in Chinese hamster ovary (CHO) cells. A potential drawback of current scRNA-seq platforms is that the cost can limit the complexity of experimental design and therefore the utility of the approach. In this manuscript, we report the use of oligonucleotide barcoding to perform multiplexed CHO cell scRNA-seq to study the impact of tunicamycin (TM), an inducer of the unfolded protein response (UPR). For this experiment, we treated a CHO-K1 GS cell line with 10μg/ml tunicamycin and acquired samples at 1, 2, 4 and 8 hr post-treatment as well as a non-treated TM-control. We transfected cells with sample-specific polyadenylated ssDNA oligonucleotide barcodes enabling us to pool all cells for scRNA-seq. The sample from which each cell originated was subsequently determined by the oligonucleotide barcode sequence. Visualisation of the transcriptome data in a reduced dimensional space confirmed that cells were not only separable by sample but were also distributed according to time post-treatment. These data were subsequently utilised to perform weighted gene co-expression analysis (WGCNA) and uncovered groups of genes associated with TM treatment. For example, the expression of one group of coexpressed genes was found to increase over the time course and were enriched for biological processes associated with ER stress. The use of multiplexed single cell RNA-seq has the potential to reduce the cost associated with higher sample numbers and avoid batch effects for future studies of CHO cell biology. Highlights ### Competing Interest Statement The authors have declared no competing interest. * CLR : center-log-ratio CHO : Chinese hamster ovary ER : Endoplasmic reticulum GO : Gene Ontology MAD : Median Absolute Deviations ME : Module Eigengene scRNA-seq : single cell RNA-seq SBO : short barcode oligonucleotide SFT : Scale Free Topology TOM : Topological Overlap Measure TM : Tunicamycin t-SNE : t-stochastic neighbour embedding UPR : unfolded protein response UMAP : uniform manifold approximation and projection WGCNA : weighted gene coexpression network analysis ssDNA : single stranded DNA