FunGen-xQTL Resources

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.

Cohort
ROSMAPReligious Orders Study and Rush Memory and Aging Project
Data type
ExpressionOmics data
Tissue or cell type
monocyte
Sample size
Not recorded on this page
Release status
Stagednot yet verified
Access
ControlledData use certificate
Lead analysts
Travyse EdwardsSelect a name to email them
QTL results
ROSMAP monocyte eQTL
Open syn22024496 in Synapse ↗

Access

Controlled access. Request data access for ROSMAP on the AD Knowledge Portal; you need a Synapse account. See How to get the data.

WhereIDAccessWhat you get
Synapsesyn22024496ControlledFiles described below

Other Synapse IDs on this page syn69670592 syn69670597 syn69670600 syn69670611 syn69670630 syn69865816

shell
pip install synapseclient
synapse login
synapse get -r syn22024496

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)

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.

These samplesa ll share the same library preparation method and are not multi-specimen samples. However, there is variety in read length, sex, and platform. It may be worthwhile to use these as covariates in the downstream analyses. I will remove the two samples that are missing sex information (though I can just impute the sex).

The biospecimen file identifies the individuals that have SNP array data, Whole Genome Sequencing data, or both available. An overlapping check confirmed the monocyte gene expression contains a mix of SNP array and whole genome sequencing data (with a lot of overlap between the two). With in the 614 samples for which we have the expression data for, 246 are overlapped with WGS, 313 are overlapped with SNP array and 239 are overlapped with joint-call WGS.

Study Metadata

  • PI: David A. Bennett (Rush University Medical Center, Chicago, IL, USA)
  • Grant numbers: 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.
  • Omics data: syn22024496
  • Genetics data: ng00067

QTL Analysis

QTL analysis for this dataset is documented in ../../qtl/eQTL/ROSMAP_monocyte_expression_qtl.md.

Flagship paper analyses: