ROSMAP Single-Nucleus Alternative Splicing QTL (snSplicing)#

Single-nucleus alternative splicing QTL analysis from CUIMC & MIT harmonized snRNA-seq / Multiome data across seven major cell types.

Please refer to this document for an overview of the ROSMAP project.

Contact#

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 CUIMC & MIT harmonized mega dataset (530 unique donors: CUIMC 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: CUIMC & 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 cis-QTL association testing#

  • s3://statfungen/ftp_fgc_xqtl/analysis_result/cis_association/ROSMAP/sQTL/snuc_mega/

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