Contact
katarina.ihrmark@slu.se, 018-672735
Services at UMBLA
Last changed: 04 March 2024
SLU Metabarcoding Laboratory - UMBLA has four modules; DNA extraction, Barcode amplification and sequence pool preparation, Bioinformatics analysis, and Sample and data storage. Each module is autonomous and can be utilized independently by users or in concert, providing a “hand in samples – obtain species lists” service.
1. DNA extraction
DNA extraction is a crucial step in all studies and sometimes has to be optimized for new types of samples and studies. Therefore, DNA extraction is only offered according to standard protocols or according to the user’s requested extraction protocols. We can also assist in development and optimization of new extraction methods for any kind of substrates, provided that costs for additional labor and consumables are covered by you.
2. Barcode amplification and sequence pool preparation
In this module, starting with user-provided or in-house-extracted DNA, we provide quantification and quality control, PCR amplification and preparation of samples for sequencing. To ensure high quantity and quality of all analyses, DNA extracts are analyzed by Nanodrop, Qubit and/or Bioanalyzer. UMBLA will offer size and quantification standards for DNA. DNA samples will be PCR amplified with tagged primers, and samples are then prepared for the requested sequencing method. Amplicon pools will be delivered to the user.
Sequencing of amplicon pools can be conducted at SciLifeLab using the requested sequencing technology or by other sequencing facilities. By collaborating with SciLifeLab, the most up-to-date sequence technology of choice will be used.
3. Bioinformatics analysis
Sequencing results from amplicons produced at UMBLA can be analyzed by SCATA for sexually reproducing eukaryotes and QIIME for bacteria and archaea. For the algal group of benthic diatoms, taxonomic assignment can be provided through the service of Galaxy in cooperation with R-SYST. Other software will be included on request. The service will include de-multiplexing and quality filtering, OTU picking, and preliminary taxonomic assignment. The SCATA pipeline will be complemented with more clustering algorithms during the proposed project.
4. Long-term storage
We offer storage of analyzed sequence data from amplicon pools prepared and analyzed by UMBLA and in collaboration with SLU biobank long-term storage of samples. The SLU biobank functions as a hub for integration and networking between different fields of research spanning from gut microflora over soil, wood and airborne organismal communities and functional ecology over to aquatic systems with microtomes and fishes. The SLU biobank stores both field and DNA samples.