Splicing QTL (sQTL) Resources on FunGen-AD Resources

Knight ADRC brain splicing QTL

Mon, 01 Jan 0001 00:00:00 +0000

Knight ADRC brain splicing QTL#

Contact#

Xuanhe Chen

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

MAGENTA African American blood alternative splicing QTL

Mon, 01 Jan 0001 00:00:00 +0000

MAGENTA African American blood alternative splicing QTL#

Contact#

Makaela Mews

MAGENTA Non-Hispanic White blood alternative splicing QTL

Mon, 01 Jan 0001 00:00:00 +0000

MAGENTA Non-Hispanic White blood alternative splicing QTL#

Contact#

Makaela Mews

MSBB brain alternative splicing QTL

Mon, 01 Jan 0001 00:00:00 +0000

MSBB brain alternative splicing QTL#

Contact#

Minghui Wang

Links to QTL analysis notebooks#

See notebooks in:

https://github.com/cumc/xqtl-analysis/tree/main/analysis/Wang_Columbia/MSBB/sQTL

The notebooks in this folder contain the commands and data wrangling codes for analysis of the expression data in MSBB. (data wrangling exist because not all data are processed using the xqtl-pipeline from the beginning and need to be reformatted to fit one intermediate step of the pipeline).

Association data preprocessing#

Genotype data preprocessing#

Principal component analysis for eQTL mapping#

Phenotype data preprocessing#

Covariate data preprocessing#

Association scan using TensorQTL and summary statistics standardization#

Path(s) to cis-QTL association testing#

output of TensorQTL.ipynb

ROSMAP AC alternative splicing QTL

Mon, 01 Jan 0001 00:00:00 +0000

ROSMAP AC alternative splicing QTL#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC alternative splicing.

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

Contact#

Ru Feng

Data Descriptions#

Verifying current avaliable location for the dataset now

Samples were extracted using Qiagen’s miRNeasy mini kit (cat. no. 217004) and the RNase free DNase Set (cat. no. 79254), and quantified by Nanodrop and quality was evaluated by Agilent Bioanalyzer.

ROSMAP DLPFC alternative splicing QTL

Mon, 01 Jan 0001 00:00:00 +0000

ROSMAP DLPFC alternative splicing QTL#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC alternative splicing.

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

Contact#

Shrishtee Kandoi and Xuanhe Chen (xuanhechenxhc@163.com)

Study Overview#

Study name : ROSMAP DLPFC sQTL
Study Description : Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) sQTL analysis summary statistics using the FGC xQTL pipeline.

Samples’ phenotype information (sex, age, race etc.) can be found in ROSMAP metadata, see “Other information” section in this document

ROSMAP PCC alternative splicing QTL

Mon, 01 Jan 0001 00:00:00 +0000

ROSMAP PCC alternative splicing QTL#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.

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

Contact#

Frank Grenn

Study Overview#

In progress

Sample information: ####/####_sample_attributes.csv.
Lab protocol: ####/####_lab_protocol.csv.
Computational protocol: ####/####_computational_protocol.csv.
QTL summary statistics output: ####/####.qtl_results.csv.
Fine-mapping results individual level data model: ####/####.susie.csv.
Fine-mapping results summary statistics model: ####/####.susie_rss.csv.
Colocalization with AD GWAS: ####/####.susie_coloc.csv.

Analysis Status#

TransQTL association: Need to be performed.

ROSMAP Single-Nucleus Alternative Splicing QTL (snSplicing)

Mon, 01 Jan 0001 00:00:00 +0000

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).