Processed 10X Genomics scRNA-seq data for article: Single-cell transcriptomics showed that maternal PCB exposure dysregulated ER stress-mediated cell type-specific responses in the liver of female offspring

Polychlorinated biphenyls (PCBs) are persistent environmental toxicants that bioaccumulate in the food chain and readily cross the placenta, raising concerns for developmental toxicity.  While PCB exposure has been associated with metabolic and neurodevelopmental disorders, its cell type-specific effects on liver development remain poorly understood. This study aimed to investigate how maternal exposure to an environmentally relevant Fox River PCB mixture affects liver development in female offspring at single-cell resolution. We hypothesized that developmental PCB exposure disrupts hepatic metabolic and immune function in a cell-type-specific manner.

From 2 weeks before mating, female dams were exposed to organic peanut oil mixed with organic peanut butter (vehicle, Trader Joe’s, Monrovia, CA) or the Fox River PCB mixture in vehicle (6 mg/kg body weight) once daily until pups were weaned at postnatal day (PND) 21.  Female mouse livers of the pups at PND 28 were collected.  Cryopreserved cells were thawed using a water bath at 37°C for 2 min, followed by serial dilution in DPBS until 32 ml was reached. Cells were centrifuged and resuspended in DPBS until a concentration of approximately 100 cells/μl was reached. The resuspended cells (n = 3), targeting 10 000 cells per sample, were then subject to scRNA-seq using a Chromium Next GEM single cell 3′ v3.1 kit and a Chromium X controller (10X Genomics, Pleasanton, CA) following the manufacturer’s instructions. The created libraries were then sequenced using the NovaSeq platform. Raw data were processed using the Cell Ranger v7.0 (10X Genomics, Pleasanton, CA).