Developed for human samples, scientists are finding that 10X Genomics offers advantages for sequencing everything from plants to flatworms. The David H. Murdock Research Institute (DHMRI) is helping to develop the needed protocols.
Although primarily supported for human samples, scientists in the Genomics Laboratory at the David H. Murdock Research Institute (DHMRI) are receiving requests to use the Chromium Controller and Solutions offered by 10X Genomics for everything from plants to marine animals.
To do this, DHMRI scientists are working with 10X Genomics and contracting with academic, industry and government researchers to develop new protocols to leverage the company’s advanced microfluidics and molecular barcoding for long-range whole genome sequencing, single-cell gene expressions, and immune repertoire profiling for application to a wider variety of samples.
10X employs a Super-Poisson loading process to capture high molecular weight DNA or Single Cells into GEMs (Gel Beads in Emulsion) that are subsequently used to finish libraries ready for high quality next generation sequencing using Illumina instrumentation. In genome analysis mode, these data can be applied for phasing and haplotyping of complex structural variants and de novo assemblies. In single cell mode, the instrument can be used to generate single cell transcriptome data from 100-10,000 cells per well (or roughly 80,000 cells per chip), allowing for scalable gene expression profiling from mixed cell populations to achieve a better understanding of tumor microenvironments.
The DHMRI Genomics staff have worked closely with scientists investigating flatworms and sea slugs to develop new protocols to extract and prepare fresh cells for sequencing with the Chromium Single Cell 3’ Solution. While it is possible to use frozen cells for their single cell approach, DHMRI scientists have found that the Chromium System generates the highest quality data when the cells are fresh. To ensure fresh cells for scientists using the 10X Genomics platform on rodent models, DHMRI’s Center for Laboratory Animal Sciences (CLAS), an AAALACi accredited facility directed by a board-certified, attending veterinarian, is available.
“We recognize the value of 10X Genomics products and solutions,” stated Jorge Marques Signes, PhD, DHMRI lead genomics scientist. “We’re proud to offer their technology in our Genomics Laboratory because of the versatility of the platform, and our ability to help develop new applications.”
To discuss a project, contact Steven Colman, PhD, DHMRI Chief Operating Officer.