The dataset provides gene expression values from microarray and RNA-sequencing experiments across multiple brains. The normalized microarray datasets for six brains include gene expression data processed using an improved normalization method introduced in March 2013, along with probe and sample metadata. Additionally, raw microarray data employing a historical normalization approach is available for two of the brains. RNA-sequencing datasets are provided for two brains, containing raw counts and TPM (transcripts per million) values for matched anatomic structures, alongside associated gene and sample metadata. These datasets support research on gene expression differences across brain regions and developmental stages, with access to both current and archived data enabling comparative analyses of normalization techniques.