Gene expression of PFAS exposed human liver spheroids and quality control

Per- and polyfluoroalkyl substances (PFAS) are a wide range of chemicals that are used in a variety of consumer and industrial products leading to direct human exposure. Many PFAS are chemically non-reactive and persistent in the environment, resulting in additional exposure from water, soil, and dietary intake. While some PFAS have documented negative health effects, data on simultaneous exposures to multiple PFAS (PFAS mixtures) are inadequate for making informed decisions for risk assessment. The current study leverages data from previous work in our group using Templated Oligo-Sequencing (TempO-Seq­™) for high-throughput transcriptomic analysis of PFAS-exposed primary human liver cell spheroids; herein, we determine the transcriptomic potency of PFAS in mixtures. Gene expression data from single PFAS and mixture exposures of liver cell spheroids were subject to benchmark concentration (BMC) analysis. We used the 25th lowest gene BMC as the point of departure to compare the potencies..., Data was derived as follows, 
Text copied with permission from:
Addicks GC, Rowan-Carroll A, Reardon AJF, Leingartner K, Williams A, Meier MJ, Moffat I, Carrier R, Lorusso L, Wetmore BA, et al. 2023. Per- and polyfluoroalkyl substances (PFAS) in mixtures show additive effects on transcriptomic points of departure in human liver spheroids. Toxicol Sci 194: 38–52.
 DOI: 10.1093/toxsci/kfad044
https://academic.oup.com/toxsci/article/194/1/38/7169149
Cell Culture 
3D InSightTM Human Liver Microtissues were purchased from InSphero (Brunswick, ME) in a 96 well format, with a single spheroid per well. These spheroids are a co-culture model from 10 different human liver donors including males and females and are a metabolically active system of hepatocytes and Kupffer cells. (Proctor et al. 2017; Rowan-Carroll et al. 2021). Upon arrival, culture media were replaced with InSphero Human Liver Maintenance Medium–Tox (InSphero (Brunswick, ME), and spheroids were acclimated at 37°C and 5% CO2 for 2..., , # Gene expression of PFAS exposed human liver spheroids and quality control

Methods related to experimental conditions are available at [https://doi.org/10.1093/toxsci/kfad044](https://doi.org/10.1093/toxsci/kfad044)

Log2-transformed DESeq2 normalized gene counts in a format appropriate for analysis with BMDExpress v3 software package (Phillips et al. 2019), that is freely available at [https://github.com/auerbachs/BMDExpress-3/releases](https://github.com/auerbachs/BMDExpress-3/releases).

Rmd file provides details on the data processing and quality control measures used to generate Log2-transformed DESeq2 normalized gene counts which are provided in a format appropriate for  BMD analysis. The file has annotations outlining quality control steps and provides figures for quality control measures.

The raw data used to generate this processed data is available at [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=) GSE145239 and GSE...