Fig 1. Experimental design, timeline, and tag-seq analysis pipeline.

(A) Timeline for prenatal bisphenol exposure, maternal care observations, and offspring growth, neurodevelopmental and behavioral outcomes. Offspring brains were collected at the bolded ages. (B) Tag-seq analysis pipeline for PND 10 medial prefrontal cortex and amygdala. Fastq files were filtered and trimmed using cutadapt, aligned to the rat genome using STAR, and sorted using samtools. Gene counts were compiled using bedtools and normalized using DEseq2. Differential gene expression analysis was done using DEseq2. Normalized, log-transformed counts were used for weighted gene co-expression network analysis (WGCNA) and the clustered eigengene modules were analyzed. Gene sets from eigengene module with significant main effects or interactions were extracted and analyzed for enriched GO biological processes, Transcription Factor (TF) Protein-Protein Interactions, and ENCODE and ChEA Consensus TFs from ChIP-X.