ROSMAP Single-Nucleus Alternative Splicing QTL (snSplicing)
Single-nucleus alternative splicing QTL analysis from CUIMC1 & MIT harmonized snRNA-seq / Multiome data across seven major cell types.
Please refer to this document for an overview of the ROSMAP project.
Access
Controlled access. Request data access for ROSMAP 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 |
Other Synapse IDs on this page syn69670600 syn69670611 syn69670597 syn69865816 syn69670630
pip install synapseclient
synapse login
synapse get -r syn69670592Contact
FunGen-xQTL Analysis Team
Study Overview
- Study name: ROSMAP snRNA-seq alternative splicing QTL
- Study Description: Splicing quantitative trait loci (sQTL) derived from single-nucleus RNA-seq data using the CUIMC1 & MIT harmonized mega dataset (530 unique donors: CUIMC1 N=424, MIT N=298). Splice-site usage was quantified using the ISSAC pipeline, producing per-cell-type pseudo-bulk splicing phenotypes across 7 major cell types and up to 95 subcell types (67 retained with >3,000 cells).
- Dataset: CUIMC1 & MIT harmonized (mega)
- Cell types: Excitatory neurons (Exc), Inhibitory neurons (Inh), Astrocytes (Ast), Oligodendrocytes (Oli), OPCs (OPC), Microglia (Mic), Endothelial cells (End)
Analysis Details
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
- ColocBoostDone
Read from the methods: map in this page's metadata header, the same data as the analysis coverage grid.