Transcriptomics, epigenomics and genetic dataset generated or co-generated in our lab
Resource Description PMID Web / GEO
AD Microglia FANS-sorted RNA-seq, ATAC-seq accompanied by SNParrays from over 100 adult Alzheimer’s disease cases and controls. doi: 10.1101/2021.01.25.21250099v1 Synapse
AD NeuN+/- FANS-sorted ATAC-seq (nerons and non-neurons) across 2 brain regions of over 400 adult Alzheimer’s disease cases and controls. doi:10.1101/2021.01.11.426303v1 Web
Epidiff FANS-sorted and bulk ChIP-seq data (neurons) from PFC brain region of over 500 Schizophrenia cases and controls doi:10.1101/2021.06.02.446728 UCSC
BOCA 2 FANS-sorted ATAC-seq (neurons and non-neurons) across 14 distinct brain regions of 5 adult individuals. 33149216 Web
Epimap  FANS-sorted and bulk ChIP-seq (neurons and non-neurons) across 2 distinct brain regions of Schizophrenia cases and controls 30038276 Synapse
BOCA FANS-sorted ATAC-seq (neurons and non-neurons) across 14 distinct brain regions of 5 adult individuals. 29945882 Web

BOCA2 (Brain Open Chromatin Atlas, v2) provides the maps of two neuronal (GABAergic and glutamatergic neurons) and two non-neuronal (oligodendrocytes and microglia & astrocytes) chromatin accessibility across 3 distinct brain regions of 4 adult individuals.

Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons
Hauberg ME, Creus-Muncunill J, Bendl J, Kozlenkov A, Zeng B, Corwin C, Chowdhury S, Kranz H, Hurd YL, Wegner M, Børglum AD, Dracheva S, Ehrlich ME, Fullard JF, Roussos P. Nature Communications 2020 11, 5581.



EpiXcan is a repository of transcriptome prediction and gene-trait association. It is based on a method, named as EpiXcan, that increases prediction accuracy in transcriptome imputation by integrating epigenetic data to model the prior probability that a SNP affects transcription. Please visit the database webpage by clicking on the above logo.’

Integrative transcriptome imputation reveals tissue-specific and shared biological mechanisms mediating susceptibility to complex traits
Wen Zhang, Georgios Voloudakis, Veera M. Rajagopal, Ben Readhead, Joel T. Dudley, Eric E. Schadt, Johan L.M. Björkegrn, Yungil Kim, John F. Fullard, Gabriel E. Hoffman, Panos Roussos.
Nature Communications, 2019. DOI: 10.1038/s41467-019-11874-7



GWAS2Genes is a database of how common genetic variants affect gene expressions. GWAS2Genes links common variants of GWAS loci to which genes are affected and in which direction by using eQTLs and SMR. Please visit the database webpage by clicking on the above logo.

Large-scale Identification of Common Variants Affecting Gene Expression in Traits and Diseases
Mads Engel Hauberg, Wen Zhang, Claudia Giambartolomei, Oscar Franzén, David L Morris, Timothy J Vyse, Arno Ruusalepp, the CommonMind Consortium, Pamela Sklar, Eric E. Schadt, Johan L.M. Björkegren, Panos Roussos.
Am J Hum Genet. 2017. DOI: 10.1016/j.ajhg.2017.04.016. PMID: 28552197



MOLOC (multiple-trait-coloc) is a Bayesian statistical framework that integrates GWAS summary data with multiple molecular QTL data to identify regulatory effects at GWAS risk loci.

A Bayesian Framework for Multiple Trait Colocalization From Summary Association Statistics
C. Giambartolomei, J. Z. Liu, W. Zhang, M. Hauberg, H. Shi, J. Boocock, J. Pickrell, A. Jaffe, the CommonMind Consortium, B. Pasaniuc, P. Roussos.
Bioinformatics. 2018 Mar 19.  DOI: 10.1093/bioinformatics/bty147. PMID: 29579179



BOCA (Brain Open Chromatin Atlas) provides the maps of neuronal and non-neuronal chromatin accessibility across 14 distinct brain regions of 5 adult individuals.

An atlas of chromatin accessibility in the adult human brain
Fullard JF, Hauberg ME, Bendl J, Egervari G, Cirnaru MD, Reach SM, Motl J, Ehrlich ME, Hurd YL, Roussos P.
Genome Res. 2018 Jun 26. pii: gr.232488.117. doi: 10.1101/gr.232488.117. [Epub ahead of print] PMID: 29945882