Internet address(es):

Main address: www.au.dk

Single Cell Sequencing and Library Prep System

Aarhus University wants to buy a single cell sequencing and library prep system.

The Danish Regenerative Engineering Alliance for Medicine (DREAM, www.dream.au.dk) has been focusing on conducting cutting edge research and developing transformative technologies to combat the increase incidence of human degenerative diseases. 1 such approach that the DREAM consortium has been taking is to decode the mechanism of human degenerative diseases such as cancers, diabetes, neurodegenerative diseases using Next Generation Sequencing (NGS) technology. Previously, the majority of NGS studies have been conducted using bulk samples, where genetic materials (RNA and DNA) are collected from samples which are highly heterogeneous. This leads to the failure of discovering rare mutations or specific gene signatures that only present in a small cluster of the cells in samples. Single cell sequencing, of which global gene expression or genomic DNA sequencing, has become one of the great breakthroughs in NGS technologies. However, the real outbreak of applying single cell sequencing for innovative discovery was not until the high throughput technical transformation in preparation of single cell sequencing libraries.

In our currently and future research, we will apply high throughput and automated single cell RNA sequencing, single cell CNV sequencing, and single cell ATAC to understand e.g. the heterogeneity, metabolism and inflammation of endothelial cells in human diseases (cancers, neovascularization in eyes, diabetes), to decode the interaction between endothelial cells and immune responses, to investigate smooth muscle cells in the pathogenesis of human atherosclerosis, the innate immune response to viral infections.

Criteria for the analytical instrumentation

— must be suitable for single cell RNA, CNV, ATAC, De novo Assembly, Exom sequencing, Genome sequencing, and immune profiling applications,

— for single cell RNA sequencing, must be suitable for 500 — 80 000+ cells in under 10 minutes, a capture rate of over 65 %, cell size flexibility, and doublet rate under 0,9 %,

— sing cell RNA must provide over 3 million pool barcodes,

— for single cell CNV application, must be suitable for capture up to 1 000 single cells in one reaction,

— single cell CNV application must provide accurately calls single cell CNV events at 2 Mb resolution, detects CNV events down to 100s of Kb on clusters of cells

— single cell ATAC sequencing must profile 500 to 10,000 nuclei per channel with our scalable, high-throughput solution, with recover rate up to 65 % of nuclei loaded on chips,

— for genome and deno novo assembly, much generate high-quality libraries from only 1 ng of genomic DNA, 10 Mb scaffold size and long-range accuracy,

— all libraries generated must be compatible with Illumina sequencing platforms,

— for all above applications, free and user friendly software must be provided for data analysis,

— all library prep procedures must be rapid and automated.

The Chromium Controller fulfill the above described criteria for single cell sequencing and novo NGS application and it is our assumption that there only is one company that manufactures such instrumentation. The Chromium Controller offers rapidly and efficiently automate the equivalent of 100 000 s to 1 000 000 s of pipetting steps for highly parallel sample partitioning and molecular barcoding and is suitable for single cell CNV, single cell gene expression, single cell immune profiling, single cell ATAC, genome sequencing, exome sequencing, and de novo assembly applications.

Internet address: https://erhvervsstyrelsen.dk/klagenaevnet-for-udbud

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