Linked Read Sequencing and Spatial Transcriptomics

Part of NGI Stockholms mission as a state-of-the-art facility is making novel techniques available to the research community.

Due to this, NGI is routinely running the chromium instrument from 10x genomics to utilize long range haplotyping and de novo genome assembly using the linked-reads technique developed by the company. The chromium is a microfluidic device that partitions molecules (e.g. large DNA fragments) into picoliter-scale droplets where the DNA is tagged with a unique barcode. These barcoded fragments are prepared into shotgun libraries and sequenced. The barcode information is used to link the short reads to the progenitor molecule, which allow them to be assembled into megabase-scale haplotypes that capture both phase information and complex genetic structural variation. To be able to utilize the instrument, reagent kits must be purchased from 10X genomics as they currently are the only provider of these reagent kits.

Huvudsaklig plats för byggnation/anläggning eller utförande: SciLifeLab, Solna.

Supplies to be purchased:

— visium spatial tissue optimization slide and reagent kit,

— visium spatial gene expression slide and reagent kits,

— visium spatial gene expression slide and reagent kits,

— visium accessory kit,

— visium spatial gene expression starter kit,

— chromium genome chip kit V2,

— chromium genome ht library and gel bead kit V2,

— chromium genome library kit and gel bead kit V2,

— chromium i7 multiplex kit.

Förklaring:

The chromium instrument from 10x genomics is routinely used in the operations at NGI Stockholm to utilize the unique linked-reads technology developed by the company. The reagent kits required to run the instrument are solely provided by 10x genomics as they are protected by patents (US Pat. No 9,644,204, US Pat. No 9,975,122, US Pat. No 10,053,723) and no alternatives are thus available on the market.

There are other companies offering products for spatial transcriptomics inference but their products offer targeted assays targeting a subset of distinct RNA. This stands in contrast to the visium spatial solution by 10x genomics as visium enables global expression inference for any poly-adenlylated mRNA, i.e. transciptome-wide, non-targeted spatial transciptomics. visium spatial reagent kits from 10x genomics are protected by patents (US Pat. No 10,030,261, US Pat No 9,593,365, US Pat No 9,371,598, US Pat No 10,308,982, US Pat No 9,868,979 and US Pat No 9,879,313).

Visma notice: https://opic.com/id/afoptyqomo