Transfer of de novo sequencing wet-lab and dry-lab expertise – ASCeND

ELIXIR-SI is establishing a new sequencing analysis centre (CPA) that will use new single cell (SC), NGS and ICT infrastructure, which is in the procurement phase. The equipment will be compatible/similar to the equipment at SciLifeLab (ELIXIR-SE node). The aim of the proposed project is to transfer good laboratory practices from SciLifeLab wet labs to new facilities and personnel in ELIXIR-SI. In particular, we plan to transfer knowledge on whole genome sequencing (WGS) and RNA sequencing for de novo genome sequencing application using modern NGS technologies: short-read DNA and RNA sequencing (Illumina, NovaSeq) combined with real-time long-read direct (3rd generation) DNA and RNA sequencing technology from Oxford Nanopore Technologies (PromethION, as well as 10x Genomics linked reads (Chromium). For this application, extraction of high-molecular weight (HMW) genomic DNA and RNA of high quality and quantity is essential and SciLifeLab will transfer its knowledge of this application to ELIXIR-SI as well. The obtained high-throughput NGS data will be analysed using well-established genome assembly and annotation (GAA) approaches. The selected use case will be the Carniolan honey bee (Apis mellifera carnica), a subspecies of the Western honey bee, a regional endemic subspecies in Slovenia.

Duration: 

1 January 2020 to 30 September 2020

Nodes involved: 

People involved: 

Brane Leskošek
Bengt Persson
Polonca Ferk
Marko Vidak
lucile_soler
Henrik Lantz