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

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).

多氯联苯（Polychlorinated biphenyls, PCBs）是一类持久性环境有毒污染物，可在食物链中发生生物富集，且极易透过胎盘屏障，由此引发了人们对其发育毒性的广泛担忧。尽管多氯联苯暴露已被证实与代谢紊乱及神经发育障碍存在关联，但其对肝脏发育的细胞类型特异性效应仍鲜有研究。本研究旨在以单细胞分辨率，探究母体暴露于环境相关的福克斯河多氯联苯混合物如何影响雌性后代的肝脏发育。我们提出假说：发育阶段的多氯联苯暴露会以细胞类型特异性的方式破坏肝脏的代谢与免疫功能。从交配前2周开始，实验母鼠每日接受一次暴露：载体组给予有机花生油与有机花生酱混合制剂（载体，Trader Joe’s，加利福尼亚州蒙罗维亚），暴露组给予载体中混有福克斯河多氯联苯混合物的溶液（剂量为6 mg/kg体重），直至幼崽于出生后第21天（PND 21）断奶。于出生后第28天（PND 28）采集雌性幼鼠的肝脏组织。将冻存细胞置于37℃水浴中解冻2分钟，随后用Dulbecco's磷酸盐缓冲液（DPBS）进行梯度稀释，直至总体积达32 mL。离心收集细胞后，重新用DPBS重悬，使细胞浓度约为100个/μL。随后将重悬后的细胞（n=3，每个样本目标捕获10000个细胞）按照制造商的操作流程，使用Chromium Next GEM单细胞3' v3.1试剂盒与Chromium X控制器（10X Genomics，加利福尼亚州普莱森顿）进行单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）。构建完成的文库随后采用NovaSeq平台进行测序。原始测序数据采用Cell Ranger v7.0软件（10X Genomics，加利福尼亚州普莱森顿）进行处理。