ShEEP Request for Single-Cell Next-Generation Sequencing Library Preparation System

Veterans Affairs Med Ctr San Francisco, San Francisco CA

Investigators

Abstract

A single-cell next-generation sequencing library preparation system is being requested in this ShEEP application, which consists of 1) 10X Genomics Chromium Controller and training and set up reagents; 2) a Thermo-Fisher Countess II Automated Cell Counter for quality control; and 3) a Workstation for downstream pipeline data processing and analysis. Items 1 is being requested from the ShEEP application, items 2 and 3 will be provided by the Research and Development Department at the San Francisco VA Health Care System. The assembled system will be integrated with the current Illumina NextSeq 500 sequencer at the Molecular Core and provide access to advanced technology of single cell next generation sequencing projects, including transcriptome analysis, genetic mutation screening and epigenome analysis, at single cell level. There are four Major Users and three Minor Users for this system, investigating 1) cancer heterogeneity and drug treatment responses (Major User, Chris Lau); 2) heart failure and drug treatment responses (Major User, Paul Simpson); 3) correlation of metabolism and inflammation in atherosclerosis and cardiovascular disease (Major User, Robert Raffai); 4) mechanisms of pulmonary arterial hypertension and right ventricular failure (Major User, Anthony Baker); 5) neurotrophin receptor modulation agents in traumatic brain injury and Alzheimer?s disease (Minor User, Stephen Massa); 6) mitochondrial structure and functions in oxidative stress- related diseases (Minor User, Gary Cecchini); and 7) epigenome changes in prostate cancer (Minor User, Yuichiro Tanaka). The availability of the single-cell next-generation sequencing library preparation system will provide means for these investigators to conduct research on the mechanisms of respective diseases, identify specific targets for translational applications in diagnosis, prognosis and therapeutic strategies, thereby establishing the precision medicine and personalized health care delivery for Veterans.