RNA-seq

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis

Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be …

Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

Human induced pluripotent stem cells (hiPSCs) are a powerful model of neural differentiation and maturation. We present a hiPSC transcriptomics resource on corticogenesis from 5 iPSC donor and 13 subclonal lines across 9 time points over 5 broad …

Schizophrenia risk variants influence multiple classes of transcripts of sorting nexin 19 (SNX19)

We explored the association between schizophrenia GWAS risk at locus 11q25 and local transcript expression of SNX19. We identified a prominent class of GWAS risk-associated SNX19 transcripts defined by an exon-exon splice junction. Further work suggests local epigenetic marks mediate the effect of risk variants on local SNX19 risk transcript expression.

Strategies for cellular deconvolution in human brain RNA sequencing data

Statistical deconvolution strategies have emerged over the past decade to estimate the proportion of various cell populations in homogenate tissue sources like brain using gene expression data. Here we show that several existing deconvolution …

Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia

The hippocampus formation, although prominently implicated in schizophrenia pathogenesis, has been overlooked in large-scale genomics efforts in the schizophrenic brain. We performed RNA-seq in hippocampi and dorsolateral prefrontal cortices (DLPFCs) …

Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome

We investigated the effects of smoking-exposure on prenatal and adult gene expression in the frontal cortex. We found developmentally-dependent gene expression differences between smoking-exposed and -unexposed brains. These expression differences were enriched for the gene signatures of autism spectrum disorder.