Proteomics Data on FunGen-AD Resources

EFIGA CSF proteomics

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

EFIGA CSF proteomics#

Contact#

Zining Qi

Knight ADRC brain proteomics

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

Knight ADRC brain proteomics#

Charles F And Joanne Knight Alzheimer’s Disease Research Center (Knight-ADRC)

Contact#

Zining Qi

Contact Email: zq2209@cumc.columbia.edu
Contact Affiliation : Columbia University
Contact Role : Zining Qi performed QTL analysis by using Knight proteomics

Study Overview#

PI : Carlos Cruchaga (Washington University in St. Louis)
Grant number : R01AG044546, P01AG003991, RF1AG053303, R01AG058501, U01AG058922, RF1AG058501, R01AG057777, P50AG05681, P01AG03991, P01AG026276
Publication : PMID: 38997326, PMID: 34239129
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.
Study name : ROSMAP DLPFC proteomics analysis
Study Description : Performed analysis on 442 Knight proteomics samples via the ADSP FGC xQTL pipeline. The output format is prepared for pQTL analysis.
Disease : Alzheimer’s Disease
Data Citation : Omics data: ng00102; Genetics data: ng00127

Dataset Description#

Raw data#

All brain samples were collected from parietal lobe. Brain tissues (~500mg) were collected from the fresh frozen human parietal lobes. SomaScan 1.3k platform were applied to measure the brain protein. The protein levels were reported as relative units of intensity (RFU or Relative Fluorescence Unit).

Knight ADRC CSF proteomics

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

Knight ADRC CSF proteomics#

Contact#

Zining Qi

MSBB brain proteomics

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

MSBB brain proteomics#

Contact#

Minghui Wang

QTL Analysis#

QTL analysis for this dataset is documented in ../../qtl/pQTL/MSBB_proteomics_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 DLPFC protein expression

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

ROSMAP DLPFC protein expression#

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

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

Contact#

Zining Qi

Contact Email: zq2209@cumc.columbia.edu
Contact Affiliation : Columbia University
Contact Role : Zining Qi performed QTL analysis by using ROSMAP proteomics

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 protein expression
Study Description : Performed on 596 ROSMAP proteomics samples via the ADSP FGC xQTL pipeline. The output format is prepared for pQTL analysis.
Disease : Alzheimer’s Disease
Data Citation : Omics data: syn17015098; Genetics data: ng00067

Dataset Description#

Raw data#

The data released in this article were processed after sampling, quantification, and normalization. We will use the protein abundance data from ROSMAP DLPFC subjects generated via tandem mass tag isobaric labeling mass spectrometry methods for protein identification and quantification Tandem Mass Tag (TMT) Discovery Proteomics (50 batches) as phenotype for our proteomics analysis.