MARKET DIALOGUE Sequencing services

The Natural Resources Institute Finland (Luke) is a research organisation whose task is to promote competitive business based on the sustainable use of renewable natural resources, as well as wellbeing and the vitality of the countryside. Luke is conducting sequencing on animals, plants, bacterial and fungal isolates and environmental samples. Luke is using both short and long read sequencing for shotgun sequencing, targeted sequencing and sequencing of bacterial and eukaryotic genomes. The subject of the procurement is sequencing services. Luke is looking for providers for 1) Metagenomic sequences 2) Transcriptomic 3) Amplicon and metabarcoding 4) Sanger sequencing 5) Whole genome sequencing 6) Sequencing of self-made pooled libraries 7) ddRAD and ATAC Interested suppliers can take part in either one or all of the service packages., Metagenomic sequencing Provider for sequencing services for metagenomic sequences. (DNA from e.g. soil, water, ice, snow, plant air traps/root/stem, gut of the organism.) Target is metagenomic sequencing and sequencing library preparation. Both Long reads (PacBio and/or Nanopore) and short reads (Illumina/AVITI or similar) are part of this market dialogue., Transcriptomic Provider for sequencing services for transcriptomic. (RNA from e.g. soil, water, ice, snow, air, plant surface/root/stem/blood/tissue/isolates/animal gut.) Transcriptomic library preparation using mRNA (Gene expression profilling, rRNA depletion or mRNA fishing part of this process) and total RNA as starting material and also lncRNA, miRNA or small RNAs. Sequencing of libraries using Illumina/AVITI or similar. Iso-seq. using e.g. Pac-Bio., Amplicons and metabarcoding Provider for sequencing services for amplicons and metabarcoding. (The matrix is DNA.) a. Fungi b. Bacteria c. Animals, protozoa, microscopic animals d. Animal droppings (mammalian identification) e. Air samples, water, fungi, insects f. Insects g. Plants Amplicons and metabarcoding. PCR of gene of interest, including but not limited to 16S rRNA, 18S rRNA, COI, ITS from bacteria, archaea, fungi, protist, fish, mammals, insects., Sanger sequencing Provider for sequencing services for sanger sequencing of PCR-fragments., Whole genome sequencing Provider for sequencing services for whole genome sequencing. a. Viruses (DNA, RNA) b. Viruses with host (DNA and RNA) c. Plants and trees d. Bacteria e. Fungi (including nematodes) f. Vertebrate species (whole genomes) g. epigenetics h. Hi-C or Omni-C Hi-C is a powerful genomic technique used to study the three-dimensional (3D) structure of genomes by analyzing chromatin interactions within the nucleus. Omni-C is cutting-edge genomic technology build on Hi-C, overcoming limitations of the later. Both would be used to study genomes of animals, plants etc.., Sequencing of self-made pooled libraries Provider for sequencing services for sequencing of self-made pooled libraries. Sequencing of libraries which customer has prepared (e.g. metagenomes, genomes, amplicons, metatranscriptomes) using short read (Illumina, AVITI or similar) or long read (PacBio and/or Nanopore)., ddRAD and ATAC Provider for sequencing services for ddRAD and ATAC. GBS (Genotyping By Sequencing) to identify variations between individuals using ddRAD (double digest Restriction-site Associated DNA) to discover thousands of genetic makers (SNPs -single nucleotide polymorphism), particular for non-model organisms, e.g. fish, other animals, fungi and plants. Depending on the species different enzyme combination are necessary. ATAC-seq (Assay for Transposase-Accessible Chromatin sequencing). It is a genomic technique to map open chromatin regions within or across a genome. Those loci containing gene regulatory elements such as promotors, enhancers and transcription factor binding sites. This technique would be applied to various animals, plants and others but also to cell culture samples.,