Sequencing-Based Transcriptome Analysis Pipeline

Illumina sequencing libraries were generated with the TruSeq Stranded mRNA HT kit (Illumina) using an Eppindorf ePMotion 5075 robot and were sequenced to a depth 45–60 million reads per sample on Hi-Seq 2500 instruments at the Roy J. Carver Biotechnology Center at the University of Illinois. All sequencing data generated in this study have been deposited to the GEO database under Accession number GSE184549. Pairwise comparisons of E18, P1 and P3 samples were completed as previously described in detail [37 (link)], with results provided in S2 Table. For functional analysis, genes that were found to be differentially expressed at fdr < 0.05 were first filtered for absolute fold change >1.5, and uploaded to the ToppCluster web analysis tool [61 (link)] using default conditions (Bonferroni correction, fdr <0.05). Selected categories are summarized in Fig 2, with full ToppCluster Results reported in S3 Table.