BrainSeq Phase 2

Schizophrenia DLPFC and HIPPO

The hippocampus formation, though prominently implicated in schizophrenia pathogenesis, has been overlooked in large-scale genomics efforts in schizophrenic brain. We performed RNA-seq in the hippocampus and dorsolateral prefrontal cortex (DLPFC) from 551 individuals (286 with schizophrenia). We identified substantial regional differences in gene expression, and found widespread developmental differences that were independent of cellular composition. We identified 48 and 245 differentially expressed genes (DEG) associated with schizophrenia within hippocampus and DLPFC, with little overlap between the brain regions. Of schizophrenia GWAS risk loci, 124/163 (76.6%) contained eQTLs in any region. Transcriptome-wide association studies in each region identified many novel schizophrenia risk features that were brain region-specific. We lastly identified potential molecular correlates of in vivo evidence of altered prefrontal-hippocampal functional coherence in schizophrenia. These results underscore the complexity and regional heterogeneity of the transcriptional correlates of schizophrenia and offer new insights into potentially causative biology.

Processed Data

These are RangedSummarizedExperiment R Objects processed against hg38 with Gencode v25.

Processed Results

For more details about these files and their contents, please check the BrainSeq Phase II README.

Raw Data

  • RNA-seq reads: FASTQ via Globus collections jhpce#bsp2-dlpfc and jhpce#bsp2-hippo. See this page at the JHPCE knowledge base for instructions on how to use Globus.
  • Phenotype data: RData. This demographic table, which includes cell RNA fraction estimates, can be used to replace the colData() slot of the RangedSummarizedExperiment objects.
  • Genotype data: dbGaP - we will share analysis-ready genotype data with researchers that obtain dbGaP access of that accession.

Check the corresponding scripts or use GitHub's search feature to find where each of the R objects were created. If you have questions about the files, please open an issue.

This site describes data and resources for the BrainSeq Phase 2 DLPFC and HIPPO resource paper which you can cite below:

Collado-Torres L, Burke EE, Peterson A, Shin JH, Straub RE, Rajpurohit A, Semick SA, Ulrich WS, BrainSeq Consortium, Valencia C, Tao R, Deep-Soboslay A, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE. Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia. bioRxiv, DOI 10.1101/426213. 2018. Pre-print URL.

Analysis code is available on GitHub.