RNA Splicing Data on FunGen-AD Resources

Knight ADRC brain splicing

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

Knight ADRC brain splicing#

Contact#

Xuanhe Chen

Study Metadata#

PI: Carlos Cruchaga (Washington University in St. Louis)
Grant numbers: R01AG044546, P01AG003991, RF1AG053303, R01AG058501, U01AG058922, RF1AG058501, R01AG057777, P50AG05681, P01AG03991, P01AG026276
Publication: PMID: 38997326, PMID: 31591557
Genetics publication: PMID: 38997326
Acknowledgement: This work was supported by grants from the National Institutes of Health (R01AG044546, P01AG003991, RF1AG053303, R01AG058501, U01AG058922, RF1AG058501 and R01AG057777). The recruitment and clinical characterization of research participants at Washington University were supported by NIH P50 AG05681, P01 AG03991, and P01 AG026276. This work was supported by access to equipment made possible by the Hope Center for Neurological Disorders, and the Departments of Neurology and Psychiatry at Washington University School of Medicine.
Omics data: ng00083
Genetics data: ng00127

QTL Analysis#

QTL analysis for this dataset is documented in ../../qtl/sQTL/Knight_ADRC_brain_splicing_qtl.md.

MAGENTA African American blood alternative splicing

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

MAGENTA African American blood alternative splicing#

Contact#

Makaela Mews

MAGENTA Non-Hispanic White blood alternative splicing

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

MAGENTA Non-Hispanic White blood alternative splicing#

Contact#

Makaela Mews

MSBB brain alternative splicing

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

MSBB brain alternative splicing#

Contact#

Minghui Wang

QTL Analysis#

QTL analysis for this dataset is documented in ../../qtl/sQTL/MSBB_brain_splicing_qtl.md.

Flagship paper analyses:

Fine-mapping (SuSiE-RSS): syn69670592
TWAS weight models: syn69670600
Quantile TWAS (qTWAS) models: syn69670611
Multi-context colocalization (ColocBoost): syn69670597
AD GWAS–xQTL colocalization results: syn69865816
AD GWAS–xQTL colocalization models: syn69670630

ROSMAP AC alternative splicing

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

ROSMAP AC alternative splicing#

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#

Frank Grenn

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

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

ROSMAP DLPFC alternative splicing#

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#

Xuanhe Chen; Shrishtee Kandoi

Contact Email : xuanhechenxhc@163.com;
Contact Affiliation : Columbia University; Boston University
Contact Role : Xuanhe Chen performed sQTL analysis via psichomics package, and SuSiE uni-variate fine-mapping analysis using psichomics sQTL data, Shrishtee Kandoi performed sQTL analysis via leafCutter package.

Study Overview#

PI : David A. Bennett (Rush University Medical Center, Chicago, IL, USA)
Grant number : U01AG046152, R01AG048015, U01AG061356, R01AG15819, U01AG061359
Publication : PMID: 30084846
Genetics Publication : PMID: 40407102
Acknowledgement : Study data were generated from postmortem brain tissue provided by the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) cohort at Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago.
Study name : splicing phenotype processing using ROSMAP DLPFC RNAseq Bulk Brain
Study Description : From STAR alignment output of ROSMAP DLPFC RNAseq Bulk Brain data (sample size 1141), we used leafCutter package to find intron usage ratio data for intron clusters and psichomics package to find percent spliced in (PSI) values for different alternative splicing events. All phenotype processing was done using the ADSP FGC xQTL pipeline and the output format is prepared for sQTL analysis.
Disease : Alzheimer’s Disease
Data Citation : Omics data: syn3388564; Genetics data: ng00067
Additional study information :

Dataset Details#

Raw data#

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 PCC alternative splicing

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

ROSMAP PCC alternative splicing#

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

Contact#

Frank Grenn

Study Overview#

Study information: study_info/ROSMAP.md
Website&Logo : https://www.synapse.org/#!Synapse:syn3157322

Dataset Details#

Raw data#

Path(s) on HPC:

PCC RNASeq data from Zhang Lab, /restricted/projectnb/casa/skandoi/ROSMAP_PCC_AC:

$ ls -lh rnaseqc_call_PCC/*.bam | head
-rw-r--r-- 1 skandoi casa 4.0G Dec 11 18:27 1000-PCC.bam.Aligned.sortedByCoord.out.md.bam
-rw-r--r-- 1 skandoi casa 3.5G Dec 9 15:22 1000-PCC.bam.Aligned.toTranscriptome.out.bam
-rw-r--r-- 1 skandoi casa 5.5G Dec 11 18:35 1001-PCC.bam.Aligned.sortedByCoord.out.md.bam
-rw-r--r-- 1 skandoi casa 4.1G Dec 9 15:25 1001-PCC.bam.Aligned.toTranscriptome.out.bam
-rw-r--r-- 1 skandoi casa 4.5G Dec 11 18:29 1002-PCC.bam.Aligned.sortedByCoord.out.md.bam
-rw-r--r-- 1 skandoi casa 4.2G Dec 9 15:23 1002-PCC.bam.Aligned.toTranscriptome.out.bam
-rw-r--r-- 1 skandoi casa 5.1G Dec 11 18:33 1003-PCC.bam.Aligned.sortedByCoord.out.md.bam
-rw-r--r-- 1 skandoi casa 1.5G Dec 9 15:22 1003-PCC.bam.Aligned.toTranscriptome.out.bam
-rw-r--r-- 1 skandoi casa 5.5G Dec 11 18:39 1004-PCC.bam.Aligned.sortedByCoord.out.md.bam
-rw-r--r-- 1 skandoi casa 1.1G Dec 9 15:22 1004-PCC.bam.Aligned.toTranscriptome.out.bam

Molecular phenotype matrices#

Path(s) on HPC:

ROSMAP snRNA-seq Splicing (ISSAC)

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

ROSMAP snRNA-seq Splicing (ISSAC)#

Single-nucleus RNA-seq splicing QTL analysis using the ISSAC (Integrative Single-cell Splicing Analysis with Context) method, applied to harmonized CUIMC and MIT single-nucleus data from ROSMAP DLPFC.

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

Contact#

FunGen-xQTL Analysis Working Group

Study Overview#

PI: Phil De Jager (Columbia University) and Manolis Kellis (Massachusetts Institute of Technology)
Grant numbers: U01AG061356, RF1AG057473, U01AG046152, R01AG066831, U01AG072572, AG058002, AG062377, NS110453, NS115064, AG062335, AG074003, NS127187, MH119509, HG008155, RF1AG062377, RF1AG054321, RO1AG054012, GM087237, P30AG10161, P30AG72975, R01AG15819, R01AG17917, U01AG46152, U01AG61356
Publication: PMID: 38514782, PMID: 39048816, PMID: 37774677, PMID: 40060644
Genetics publication: PMID: 40407102
Acknowledgement: Study data were generated from postmortem brain tissue provided by the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) cohort at Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago. This work was funded by NIH grants U01AG061356 (De Jager/Bennett), RF1AG057473 (De Jager/Bennett), and U01AG046152 (De Jager/Bennett) as part of the AMP-AD consortium, as well as NIH grants R01AG066831 (Menon) and U01AG072572 (De Jager/St George-Hyslop). This work was also supported in part by the Cure Alzheimer’s Fund, NIH grants AG058002, AG062377, NS110453, NS115064, AG062335, AG074003, NS127187, MH119509, HG008155 (M.K.), RF1AG062377, RF1AG054321, RO1AG054012 (L.-H.T.) and the NIH training grant GM087237 (to C.A.B.). ROSMAP is supported by P30AG10161, P30AG72975, R01AG15819, R01AG17917, U01AG46152, U01AG61356.
Omics data: syn31512863 (CUIMC), syn52293417 (MIT)
Genetics data: ng00067
Disease: Alzheimer’s Disease

Dataset Details#

Cohort and Sample Overview#

This study utilized single-nucleus RNA sequencing data from the dorsolateral prefrontal cortex (DLPFC, Brodmann Area 9) of post-mortem human brain tissue from two cohorts as part of the FunGen-xQTL harmonized aging brain resource project: