FunGen-xQTL Resources

MetaBrain Brain Gene Expression QTL

MetaBrain multi-region bulk RNA-seq gene expression data used for validation of eQTL signals in the FunGen-xQTL flagship study.
Cohort
MetaBrainExternal bulk brain eQTL replication resource
Modality
eQTLQTL results
Tissue or cell type
5 brain regions
Sample size
Not recorded on this page
Release status
Stagednot yet verified
Lead analysts
FunGen-xQTL Analysis TeamContact by name
Source data
MetaBrain Expression
Open syn69670592 in Synapse ↗ Query associations in the xQTL Atlas ↗

Access

Controlled access. Request data access for MetaBrain on the AD Knowledge Portal; you need a Synapse account. See How to get the data.

WhereIDAccessWhat you get
Synapsesyn69670592ControlledResults described below

Other Synapse IDs on this page syn69670600 syn69670611 syn69670597 syn69865816 syn69670630

shell
pip install synapseclient
synapse login
synapse get -r syn69670592

Contact

FunGen-xQTL Analysis Team

Study Overview

  • Study name: MetaBrain brain expression eQTL
  • Study Description: Large-scale brain eQTL meta-analysis across five brain regions used as a validation and replication resource. All five MetaBrain contexts were used to replicate xQTL signals identified in the ROSMAP, MSBB, and MiGA cohorts.
  • Brain regions: Cerebellum, Cortex, Basal ganglia, Spinal cord, Hippocampus
  • Reference: Schipper et al. 2021, Nature Neuroscience. doi:10.1038/s41593-021-00976-7

Analysis Details

MetaBrain summary statistics were obtained from the MetaBrain resource and used as an independent eQTL replication dataset in the FunGen-xQTL flagship analysis. Fine-mapping and colocalization were performed in parallel with the primary FunGen-xQTL datasets.

See MetaBrain processing notebooks in:

Path(s) to summary statistics

Path(s) to fine-mapping with SuSiE RSS model

Fine-mapping model objects (SuSiE-RSS, .rds) are available in the finemapping models folder (syn69670592).

Path(s) to TWAS models

Pre-trained TWAS weight models for this context: syn69670600

Quantile TWAS (qTWAS) models: syn69670611

Path(s) to colocalization with SuSiE-coloc / ColocBoost

Multi-context colocalization models (ColocBoost): syn69670597

AD GWAS–xQTL colocalization results: syn69865816

AD GWAS–xQTL colocalization models: syn69670630

Analyses

  • cis-QTLDone
  • SuSiEDone

Read from the methods: map in this page's metadata header, the same data as the analysis coverage grid.