RNA-Seq of homo sapiens; whole human cerebral organoids
Pooled male and female VEH (n=3) and 0.1 M nicotine-treated (n=3) organoids were snap frozen and sent to Genome Quebec (Montreal, Quebec, Canada) for total RNA extraction, library preparation and RNA-Seq. Quality checks were performed by Genome Quebec following extraction and library preparation. The RNA integrity number was used to assess RNA quality and all samples had RNA integrity number scores  7.0. Paired-end reads (25 million) were sequenced on the Illumina NovaSeq platform. All raw reads were aligned and annotated with the latest ENSEMBL Homo Sapien GRCH38.p13 reference genome using STAR version 2.7.10a with recommended settings. Raw counts were generated using the Rsubread subpackage featureCounts. Lowly expressed genes were filtered out using a count per million cutoff of 0.4 in at least 2 or more samples. Normalization and DE analysis were done using the edgeR package