Gene Expression Data on FunGen-AD Resources

Knight ADRC brain gene expression

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

Knight ADRC brain gene expression#

Contact#

Chunming Liu

Study Overview#

Study information: descriptor/study_info/KnightADRC.md.
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/eQTL/Knight_ADRC_brain_expression_qtl.md.

MAGENTA African American blood gene expression

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

MAGENTA African American blood gene expression#

Multi-Ancestry Genomics, Epigenomics, and Transcriptomics of Alzheimer’s (MAGENTA) Project: Participants include 465 individuals (AA – 113 with AD, 118 cognitively intact controls; NHW – 116 with AD, 118 controls) ascertained by the John P. Hussman Institute for Human Genomics (HIHG) at the University of Miami Miller School of Medicine (Miami, FL), North Carolina A&T State University (Greensboro, NC), and Case Western Reserve University (Cleveland, OH). Participants were ascertained as part of the ADSP Follow-up Study and included both cases (>65 years of age of onset) and controls (>65 years of age at age of exam). All participants were adjudicated by a clinical panel with expertise in AD related disorders and classified as AD according to standard criteria developed by the National Institute of Aging and the Alzheimer’s Association.

MAGENTA Non-Hispanic White blood gene expression

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

MAGENTA Non-Hispanic White blood gene expression#

MetaBrain Brain Expression

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

MetaBrain Brain Expression#

Summary#

MetaBrain is a large-scale meta-analysis of brain expression data across multiple brain regions and cohorts. The resource aggregates RNA-seq data from multiple independent studies to enable robust eQTL discovery across brain regions relevant to neurological and psychiatric disorders.

Dataset Information#

Cohorts: Multiple cohorts (see MetaBrain.nl)
Brain regions: Cerebellum, Cortex, Basal ganglia, Spinal cord, Hippocampus
Data type: Bulk RNA-seq
Samples: ~2,000+ samples per region (region-specific)

Omics Data#

Gene expression matrices#

Expression matrices (TMM-normalized counts) available from MetaBrain.nl.

MiGA multi-brain region gene expression

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

MiGA multi-brain region gene expression#

A genetic and transcriptomic resource comprised of 255 primary human microglia samples isolated ex vivo from four different brain regions of 100 human subjects with neurodegenerative, neurological, or neuropsychiatric disorders, as well as unaffected controls.

The human post-mortem brain samples were obtained from the Netherlands Brain Bank (NBB) and the Neuropathology Brain Bank and Research CoRE at Mount Sinai Hospital. The permission to collect human brain material was obtained from the Ethical Committee of the VU University Medical Center, Amsterdam, The Netherlands, and the Mount Sinai Institutional Review Board. For the Netherlands Brain bank, informed consent for autopsy, the use of brain tissue and accompanied clinical information for research purposes was obtained per donor ante-mortem.

MSBB brain gene expression

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

MSBB brain gene expression#

Contact#

Minghui Wang

QTL Analysis#

QTL analysis for this dataset is documented in ../../qtl/eQTL/MSBB_brain_expression_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 gene expression

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

ROSMAP AC gene expression#

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

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 gene expression

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

ROSMAP DLPFC gene expression#

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

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

NOTE: we didn’t perform the omics data calling here so this descriptor is mostly documentations from the raw data source

Contact#

Xuanhe Chen (xuanhechenxhc@163.com)

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 : ROSMAP DLPFC RNA-seq Bulk Brain
Study Description : 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.
Disease : Alzheimer’s Disease
Data Citation : Omics data: syn3388564; Genetics data: ng00067
Additional study information :

Dataset Details#

Library Preparation

ROSMAP PCC gene expression

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

ROSMAP PCC gene expression#

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 RNA-seq microglia gene expression

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

ROSMAP RNA-seq microglia gene expression#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) microglia data-set.

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

Contact#

Travyse Edwards

Data descriptions#

The ROSMAP monocyte data were downloaded from syn2580853 on Janunary xx, 2023.

Path on CU cluster /..

QTL Analysis#

QTL analysis for this dataset is documented in ../../qtl/eQTL/ROSMAP_microglia_expression_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 RNA-seq monocyte gene expression

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

ROSMAP RNA-seq monocyte gene expression#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) monocyte data-set.

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

Contact#

Travyse Edwards

Data descriptions#

The ROSMAP monocyte data on MSSM were downloaded from syn22024496 on July 11th, 2022. (path on MSSM to be added)

Path on MSSM cluster /sc/arion/projects/load/data-ext/ROSMAP/raw/rnaseq_monocytes_syn23650893/Gene_Expression-RNA-seq-monocyte

Preview Monocyte Gene Expression Data#

Over all 615 samples in the dataset, 302 samples have diagnosis meta data, 1 sample missing associated sex meta data.

ROSMAP snRNA-seq pseudo-bulk gene expression

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

ROSMAP snRNA-seq pseudo-bulk gene expression#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) snRNA-seq from different cells in Dorsolateral Prefrontal Cortex (DLPFC).

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

Contact#

Hao Sun and Masashi Fujita

Study Overview#

PI : Phil De Jager (Columbia University) and Manolis Kellis (Massachusetts Institute of Technology)
Grant number : 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.
Study name : ROSMAP snRNA-seq pseudo-bulk gene expression
Study Description :
Disease : Alzheimer’s Disease
Data Citation : Omics data: syn31512863 (CUIMC), syn52293417 (MIT); Genetics data: ng00067
Additional study information :

Dataset Description#

Raw data#

FIXME: need Masashi’s input here

STARNET macrophage gene expression QTL

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

STARNET macrophage gene expression QTL#

STARNET is an RNA expression study of various disease-relevant tissues obtained from living patients with cardiovascular disease (CVD). The inclusion criterion for patients was eligibility for coronary artery by-pass graft (CABG) surgery.

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

Contact#

Travyse Edwards

Contact Email: travyse.edwards@icahn.mssm.edu
Contact Affiliation: Icahn School of Medicine at Mount Sinai
Contact Role: Travyse performed QC & QTL analysis

Study Overview#

Grant Number: TBD
Publication: TBD
Acknowledgement: TBD
Study Name: STARNET Macrophage RNA-Seq Quantification
Study Description: TBD
Disease: Alzheimer’s Disease
Data Citation:
- Local Path: /sc/arion/projects/load/data-int/STARNET/raw
Additional Study Information: This data is not okay to use outside of the xQTL group.

Information to fix: