The Isoform-centric Microglia Genomic Atlas (isoMiGA) Project

Jack Humphrey, Erica Brophy, Towfique Raj lab

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The isoMiGA project combines long-read and short-read RNA-seq from microglia cells purified from post mortem human brains.

Using an atlas of novel isoforms, we show that microglia use a range of isoforms in response to stimulation and can differentiate microglia from different brain regions.

We then map genetic associations with isoform usage and other types of RNA splicing, observing that multiple GWAS variants act through novel microglia isoforms in Alzheimer's and Parkinson's disease.

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Manuscript

Preprint on MedRxiv

Raw Data

All Long-read data - deposition in progress

Gaffney short-read cohort

Raj short-read microglia samples

Roussos short-read batch 1

Roussos short-read batch 2

Stimulated IMGL short-read

Processed Data

Novel isoform GTF and FASTA

Count matrices for all cohorts

All QTL summary statistics

Pipelines

Short-read RNA-seq processing

Long-read RNA-seq processing

QTL mapping and meta-analysis

Genotype quality control

Long-read RNA-seq isoforms

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Genotype QC

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Mass spectrometry

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Differential analyses

Stimulation response

Differential gene expression

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Differential transcript usage

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Region specificity

Differential gene expression

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Differential transcript usage

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MESC

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QTL Mapping

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GWAS Colocalization

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Visualizing QTLs

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