FunGen-xQTL Resources

MiGA multi-brain region gene expression

A genetic and transcriptomic resource comprised of 255 primary human microglia samples isolated ex vivo from four different brain regions of 100 human subjects with neurodegenerative, neurological, or neuropsychiatric disorders, as well as unaffected controls.

The human post-mortem brain samples were obtained from the Netherlands Brain Bank (NBB) and the Neuropathology Brain Bank and Research CoRE at Mount Sinai Hospital. The permission to collect human brain material was obtained from the Ethical Committee of the VU University Medical Center, Amsterdam, The Netherlands, and the Mount Sinai Institutional Review Board. For the Netherlands Brain bank, informed consent for autopsy, the use of brain tissue and accompanied clinical information for research purposes was obtained per donor ante-mortem.

Cohort
MiGAMicroglia Genomic Atlas
Data type
ExpressionOmics data
Tissue or cell type
microglia, 4 regions
Sample size
Not recorded on this page
Release status
Stagednot yet verified
Access
ControlledData use certificate
Lead analysts
Travyse EdwardsSelect a name to email them
Open syn69670592 in Synapse ↗

Access

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

WhereIDAccessWhat you get
Synapsesyn69670592ControlledFiles described below

Other Synapse IDs on this page syn69670597 syn69670600 syn69670611 syn69670630 syn69865816

shell
pip install synapseclient
synapse login
synapse get -r syn69670592

Contact

Travyse Edwards

Study Overview

Dataset Description

Raw data

Molecular phenotype matrices

We have gene expression data for four brain regions: medial frontal gyrus (GFM), superior temporal gyrus (GTS), thalamus (THA), and subventricular zone (SVZ). I have included information about the TPM matrices below for each brain region. The columns are sample names and the rows are gene ids.

  • GFM
    • File: sample-gfm.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz
    • Columns: 75, Rows: 45814
  • GTS
    • File: sample-gts.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz
    • Columns: 63, Rows: 45472
  • THA
    • File: sample-tha.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz
    • Columns: 61, Rows: 45461
  • SVZ
    • File: sample-svz.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz
    • Columns: 53, Rows: 42086

File Sizes:

Other Key Files

TBD

  1. EDA: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Marcora_MSSM/MiGA/data_overview.ipynb
  2. Molecular Phenotype Calling
  3. Genotype Preprocessing
  4. Phenotype Preprocessing
  5. Covariate Preprocessing
  6. Association Scan

QTL Analysis

QTL analysis for this dataset is documented in ../../qtl/eQTL/MiGA_brain_expression_qtl.md.

Flagship paper analyses: