ShEEP request for Chromium Controller

Oklahoma City Va Medical Center, Oklahoma City OK

Investigators

Abstract

We are requesting funds to purchase a 10X Genomics Chromium System. This instrument allows investigators to perform gene expression analysis on single cells and structural genomic analysis of (SNPs, deletions, transitions, etc) through genome sequencing of large scaffolds. Currently, neither the research facility at the Oklahoma City VA Medical Center (OKC VAMC) or the affiliated University of Oklahoma Health Sciences Center have the ability to measure gene expression/genomic integrity in single cells. It is well known that cell-cell communication is important in tissue function. However, it is only now becoming evident that changes in cell heterogeneity even between the same types of cells can be potentially harmful to tissues and an organism, i.e., conditions that lead to large cell to cell differences can compromise the function of a tissue. However, in the past there was no technology available that allowed investigators to study molecular processes in large numbers of individual cells. The 10X Genomics Chromium System is a new approach to making next-generation-sequencing libraries. The Gemcode technology behind this system enables the instrument to simultaneously make thousands of mini-libraries per sample in oil droplets. One cell is captured in each droplet and the RNA-Seq library from each droplet is given a unique barcode. This allows an investigator to perform RNA-Seq on all the mini-libraries from a single cell simultaneously and separate the data after the fact. Therefore, one can characterize the individual transcriptomes on a large number of cells and determine the variance in the transcription profile of cells from a culture or tissue. The 10X Genomics Chromium System can also be used to characterize the genomic integrity of individual cells, i.e., structural variation such as deletions, transversions, rearrangements, etc. within the nuclear genome and the mitochondrial genome through individually barcoded large genomic scaffolds (50kb to 10Mb). Unlike short-read sequencing currently used in genomic studies that can be difficult to assemble into whole genomes these scaffolds are large and are more readily assembled. With the large scaffolds important structural variations are readily resolved with important implications for DNA damage, transgenic animal validation and potential in development of novel epigenomic workflows. A survey of all VA researchers at OKC VAMC showed over 80% of the researchers are interested in the potential of in using the 10X Genomics Chromium System to study the heterogeneity of cells in their research. This instrument will be used by eight major users who have VA Merit grants funded (7) or pending (1) and three potential users who have VA Merit grants funded (2) or pending (1). We also anticipate that researchers at other VA Centers will use this instrument.