One of the most significant challenges for understanding genetic control of blood pressure (BP) is that the vast majority of BP-associated single nucleotide polymorphisms (SNPs) in humans are located in noncoding regions of DNA. The major objective of this PPG is to understand the functional relevance of BP-associated noncoding SNPs in specific BP relevant cell types using epigenomics and genome editing. A key approach that all three projects of this PPG have adopted to accomplish this objective is the application of next-generation sequencing (NGS) technologies. These include RNA-seq (to analyze mRNA and lncRNA profiles), small noncoding RNA-seq (i.e., sncRNA-seq, to analyze microRNA profiles), RRBS (to measure DNA methylation patterns), ATAC-seq (to determine chromatin accessibility), CUT&Tag (to detect DNA-protein interactions) and Hi-C (to uncover chromatin interactions). The goal of Core B is to provide the highly specialized expertise required for these analyses. Over five years, three projects of this PPG will analyze 725 RNA-seq, 20 sncRNA- seq, 65 RRBS, 20 Hi-C, 155 CUT&Tag and 65 ATAC-seq libraries. Sample and library preparation will be carried out by the staff of individual projects. Cluster generation and sequencing will be performed by the well- established MCW Sequencing Service Center via fee-for-service. The role of Core B is coordinating sequencing activities to improve efficiencies and performing the vast majority of the data analysis including the processing and mapping of the sequence reads, identification and quantification of transcripts or CpG regions, calling peaks of DNA-protein interaction, chromatin interaction and accessibility, integrative analysis of omics data and downstream analysis (e.g., gene ontology and biological pathways). The Core therefore has two specific aims.
Aim 1 is to coordinate the multiplexing and submission of NGS libraries for sequencing.
Aim 2 is to analyze and manage sequencing data for all three projects. Core B Director P. Liu, Co-Investigator M. Liang and Y. Liu were founding members of an interest group initiated by Dr. Liang in 2010 and involving 12 laboratories from seven departments at MCW that adopted NGS technologies to analyze RNA and later RRBS and other NGS applications at MCW. The wet lab and dry lab pipeline established as a result of this effort has been used in > 20 publications. Importantly, this group has published some of the first studies of mRNA, lncRNA, miRNA, DNA methylation and chromatin conformation in hypertension research that utilized RNA-seq, sncRNA-seq, RRBS and chromatin conformation capture. Therefore, Core B has the experience and the highly specialized expertise to ensure the success of these omics data analyses that are critical components of the three projects.
