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 understanding of transcriptional heterogeneity in monoclonal antibody producing Chinese hamster ovary (CHO) cell line. A potential drawback of current scRNA-seq platforms is that the cost can limit the complexity of experimental designs and/or multiple runs can result in serious batch effects. 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 10ug/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 from each sample with a distinct polyadenylated ssDNA oligonucleotide barcode before pooling all samples for scRNA-seq.