MiGA multi-brain region gene expression

MiGA is a genetic and transcriptomic resource of 255 primary human microglia samples, isolated ex vivo from four brain regions of 100 donors. Donors have neurodegenerative, neurological or neuropsychiatric disorders, or are unaffected controls.

Post-mortem brain samples come from the Netherlands Brain Bank (NBB) and the Neuropathology Brain Bank and Research CoRE at Mount Sinai Hospital. The Ethical Committee of the VU University Medical Center (Amsterdam) and the Mount Sinai Institutional Review Board approved collection of the human brain material. NBB obtained informed consent from each donor before death for autopsy and for research use of brain tissue and clinical information.

Access

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

Where	ID	Access	What you get
Synapse	syn69670592	Controlled	Results described below

shell

pip install synapseclient
synapse login
synapse get -r syn69670592

Contact

Travyse Edwards

Study Overview

Study information is in MiGA study info.
Sample set and logo are at dss.niagads.org/sample-sets/snd10022.

Dataset Description

Raw data

Molecular phenotype matrices

Gene expression is available for four brain regions: medial frontal gyrus (GFM), superior temporal gyrus (GTS), thalamus (THA), and subventricular zone (SVZ). Each region has a TPM matrix with gene IDs in rows and sample names in columns. Low-expression genes and outlier samples were removed.

Region	Samples (columns)	Genes (rows)	File size
GFM	75	45,814	11 MB
GTS	63	45,472	8.8 MB
THA	61	45,461	8.6 MB
SVZ	53	42,086	6.8 MB

Other key files

None are listed yet.

Analysis notebooks

QTL analysis

The QTL analysis of this dataset is documented in MiGA brain expression QTL.

The flagship paper analyses on the AD Knowledge Portal are listed below.

Fine-mapping (SuSiE-RSS), syn69670592
TWAS weight models, syn69670600
Quantile TWAS (qTWAS) models, syn69670611
Multi-context colocalization (ColocBoost), syn69670597
AD GWAS and xQTL colocalization results, syn69865816
AD GWAS and xQTL colocalization models, syn69670630