ROSMAP RNA-seq monocyte QTL

ROSMAP RNA-seq monocyte QTL #

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. 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.