HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development.

Abstract

This paper describes a new resource, HDBR (Human Developmental Biology Resource) Expression, for studying prenatal human brain development. It is unique in the age range (4 post conception weeks [PCW] to 17PCW) and number of brains (172) studied, particularly those under 8PCW (33). The great majority of the samples are karyotyped. HDBR Expression is also unique in that both the large-scale data sets (RNA-seq data, SNP genotype data) and the corresponding RNA and DNA samples are available, the latter via the MRC-Wellcome Trust funded HDBR1(Gerrelli et al., 2015). There are 557 RNA-seq datasets from different brain regions, the majority between 4 and 12PCW. During this time the major brain regions are established and the early stages of cortex development occur (Bystron et al., 2008; O'Rahilly and Muller, 2008). In addition, there are 42 RNAseq data sets from spinal cord and 29 from cerebral choroid plexus. There are also 243 additional tissue specimens in paraffin wax blocks available for individual gene expression studies. For almost all of the brains and specimens in wax blocks there are corresponding SNP genotype data. Large-scale/high-throughput studies, such as next-generation sequencing, are providing raw material in a wide variety of research fields (for review of concepts and methodologies of RNA-seq, see Shin et al., 2014). Studies of human development are hampered by difficulties in obtaining tissue which means that publicly available large-scale data sets are particularly useful because data can be used and re-used (Kang et al., 2011; Zhang et al., 2011; Fietz et al., 2012; Miller et al., 2014; Darmanis et al., 2015).