NHP Systems Biology HTMP

University Of Washington, Seattle WA

Investigators

Linked publications, trials & patents

Abstract

NHP SYSTEMS BIOLOGY: HIGH-THROUGHPUT MOLECULAR PROFILING CORE PROJECT SUMMARY The High-throughput Molecular Profiling Core is operated by the Division of Nonhuman Primate Systems Biology to provide the resources needed for obtaining datasets by next-generation sequencing, oligonucleotide microarray, and mass spectrometry. The Core has specific expertise in applying these methods to nonhuman primate research, particularly in the area of pathogen-host interactions and serves as an incubator for technology development and for devising molecular profiling methods to study novel areas of biology. These resources support both internal and external studies and they can be accessed by external investigators through collaboration with Division scientists or directly through the Core using a fee-for-service mechanism. The Specific Aims for the Core are: 1) Provide transcriptomic profiling methods for the quantification of gene expression. A full range of services are provided, from initial RNA isolation to final datasets. The majority of transcriptional profiling is conducted by RNA-seq, with samples run on either an Illumina MiSeq or an Illumina NextSeq 500 instrument. Sequencing can be tailored to yield information on mRNA, small noncoding RNA, or total RNA (mRNA and long noncoding RNA) expression. Analysis pipelines are in place for mapping reads to current sequence databases, including available nonhuman primate genomic data. The core is active in developing new methodologies and in applying transcriptomic profiling to new research areas, including analyzing the expression of MHC genes and noncoding RNAs. Microarray profiling, using the Agilent platform, is also available. 2) Provide sequencing and data processing methods for microbiome profiling. Given the increasingly recognized role of the microbiome in health and disease, microbiome profiling is becoming an important component of experimental protocols that use nonhuman primates, particularly in infectious disease and vaccine research. The Core provides bacterial 16S ribosomal gene sequencing and data processing methods for microbiome profiling. We also provide microbial RNA-seq to identify metabolically active species of bacteria. 3) Provide mass spectrometry methods for epigenetic, proteome, phosphoproteome, and metabolome profiling, in collaboration with Dr. Ben Garcia (University of Pennsylvania). Profiling of epigenetic modifications, and of protein and metabolite abundance, provides investigators with unique insights into biological systems that cannot be obtained through transcriptomic profiling alone. These data can also be used in conjunction with transcriptomic data to provide a more comprehensive view of a biological system. The Core provides sample preparation, sample fractionation, multiple mass spectrometry platforms, and a complete data analysis pipeline.