Transcriptomics, epigenomics and genetic dataset generated or co-generated in our lab
| Resource | Description | Manuscript | Resource |
| PD snRNA-seq | snRNA-seq from 100 Parkinson’s disease cases and controls x 5 brain regions (= 500 samples) | In preparation | AMP-PD portal |
| AD Microglia (FANS); Release #2 |
FANS-sorted RNA-seq accompanied by SNParrays from over 189 adult Alzheimer’s disease cases and controls. | ResearchSq | Synapse |
| AD Microglia (scRNA-seq) | scRNA-seq on FANS-sorted myeloid cells from 137 postmortem brains (number of cells: 543,012) | MedRxiv | Synapse |
| Brain Development 3D genome |
ATAC-seq, RNA-seq, H3K4me3/H3K27ac/H3K27me3 ChIP-seq, and Hi-C from Fetal (4 individuals) and FANS-sorted adult (6 controls) postmortem brains. RNA-Seq and Hi-C of scrambled and CNTNAP2 knockdown IPSC-derived neurons. | Pubmed | Synapse |
| BED GWAS | BED GWAS summary statistics from the MVP data. | Pubmed | dbGaP |
| MS_snRNAseq | single-nucleus RNA-seq data from 6 multiple sclerosis cases and 6 controls. | Pubmed | GEO |
| Developing cerebral cortex | Multi-omics dataset (snRNA-seq + snATAC-seq) of 45,549 cortical nuclei across 6 broad developmental time-points from fetus to adult. | Pubmed | UCSC SCP CELLxGENE GEO |
| BOCA 3 | FANS-sorted RNA-seq and ATAC-seq (neurons and non-neurons) across 25 distinct brain regions of 6 adult individuals. | BioRxiv | Web GEO |
| LMNA | ATAC-seq in wild-type mice and knockdown LMNA mice. | Pubmed | GEO |
| AD Microglia (FANS) Release #1 |
FANS-sorted RNA-seq, ATAC-seq accompanied by SNParrays from over 100 adult Alzheimer’s disease cases and controls. | Pubmed | Synapse |
| PHG FANS (3 cell types) ATAC-seq, RNA-seq |
FANS-sorted ATAC-seq and RNA-seq on neurons, oligodendrocytes and microglia & astrocytes from 42 donors with AD and controls. | Pubmed | Synapse |
| AD NeuN+/- | FANS-sorted ATAC-seq (neurons and non-neurons) across 2 brain regions of over 400 adult Alzheimer’s disease cases and controls. | Pubmed | Web UCSC Synapse |
| MDD NeuN+/- | FANS-sorted ATAC-seq (neurons and non-neurons) from orbitofrontal cortex of over 30 adult MDD cases and controls. | BioRxiv | Web UCSC GEO |
| iPSC-Neuron KCl stimulation | ATAC-seq and RNA-seq in 11 iPSC-derived neurons from 6 children-onset schizophrenia cases and 5 controls. Each iPSC line is profiled in three conditions (unstimulated, 1hr and 6hr post-stimulation by KCl). | Pubmed | Web UCSC GEO |
| COVID IL10RB | RNA-seq of iPSC-derived neural progenitor cells from 3 donors in multiple conditions to validate that up-regulation of IL10RB and higher IL10RB expression in COVID-19 patient blood is associated with worse COVID-19 outcomes. | Pubmed | GEO |
| COVID brain transcriptome | snRNAseq of human brain tissue from patients with coronavirus disease and controls. | Pubmed | GEO |
| Multi-omics AD supercontrols | FANS-sorted ATAC-seq, ChIP-seq H3K4me3 & H3K27ac and RNA-seq (neurons and non-neurons) of 5 human brain regions from 10 “control” donors, i.e. without any neuropsychiatric or neurodegenerative diagnosis. | Pubmed | Synapse |
| Epidiff | FANS-sorted (neurons) and bulk ChIP-seq data from PFC brain region of over 500 Schizophrenia cases and controls | Pubmed | UCSC Synapse |
| iPSC-Microglia | ATAC-seq in 3 hiPSC-derived microglia lines. | Pubmed | GEO |
| Striatal striosome profiling | ATAC seq from EGFP+ and EGFP- cells from postnatal day 3 striatum from GENSAT Nr4a1-EGFP mice | Pubmed | GEO |
| SCZ organoids | ATAC-seq assay in 5 human developmental cortical interneurons (MGE organoid) and 2 glutamatergic neurons (CO organoid) derived from healthy control vs schizophrenia iPSCs. | Pubmed | GEO |
| BOCA 2 | FANS-sorted ATAC-seq (neurons and non-neurons) across 14 distinct brain regions of 5 adult individuals. | Pubmed | Web UCSC GEO |
| Epimap | FANS-sorted and bulk ChIP-seq (neurons and non-neurons) across 2 distinct brain regions of Schizophrenia cases and controls | Pubmed | Synapse |
| BOCA | FANS-sorted ATAC-seq (neurons and non-neurons) across 14 distinct brain regions of 5 adult individuals. | Pubmed | Web UCSC GEO |
| Prefrontal cortex profiling | FANS-sorted ATAC-seq (neurons and non-neurons) in frontopolar prefrontal cortex of 8 adult individuals. | Pubmed | GEO |
| Neat1 -/- mice profiling | Cerebral frontal cortex mRNA profiles of 2-4 months old wild type and Neat1 -/- mice (all females) generated by deep sequencing (N=5 controls; N=4 Neat1 knockout). | Pubmed | GEO |
Computational tools, servers, and databases
| Visit our Github for the most updated list of tools! | |||
| Resource | Description | Manuscript | Web / Github |
| zenith | Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream (also mentioned in the list of software in this table) by considering the correlation between gene expression traits. | In preparation | Github |
| remaCor | Method for random effects meta-analysis for correlated test statistics. | In preparation | Github |
| crumblr |
crumblr package enables analysis of count ratio data using precision-weighted linear (mixed) models, PCA and clustering. | In preparation | Github |
| dreamlet | Dreamlet is a method that uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster. | BioRxiv | Github |
| decorate | Decorate (differential epigenetic correlation test) identifies correlated epigenetic features and finds clusters of features that are differentially correlated between two or more subsets of the data. | Pubmed | Github |
| dream | Method for differential expression analysis employing repeated measures designs. | Pubmed | Bioconductor Vignette |
| mmQTL | mmQTL is a statistical package applying meta-analysis to detect multiple QTL signals integrating signals among conditions, with control for population structure and relatedness. | Pubmed | Web Github Zenodo |
| EpiXcan | 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. | Pubmed | Web |
| GWAS2Genes | 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. | Pubmed | Web |
| moloc | 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. | Pubmed | Web |