We performed strand-specific, whole transcriptome sequencing of total RNA derived from brain tissue from 120 human fetuses aged 12–19 post-conception weeks (PCW), generating a median 119 million read pairs per sample (Additional file 1: Table S1). Expression measures were derived for 144,448 Ensembl transcripts, annotated to 28,875 genes. Genomic DNA from each sample was genotyped for approximately 710,000 single nucleotide polymorphisms (SNPs), followed by genotype imputation using the Haplotype Reference Consortium r1.1 panel [16]. After strict quality control, 5.8 million SNPs were retained for analysis. Consistent with the GTEx Consortium [4], we controlled gene expression measures for latent factors using probabilistic estimation of expression residuals (PEER) [17] in addition to specified covariates and principal components from the genotyping matrix (Additional file 2: Figure S1 and Figure S2). Cis-eQTL were identified by linear regression of allele dosage against adjusted, quantile-normalized gene expression measures using FastQTL [18].
