Targeted metatranscriptomics

RNA sequencing without gene specific primers – hands in laboratory course for PhD students (2 cr)

Ribosomal RNA analysis is nowadays widely used for characterization of microbial communities in aquatic and terrestrial ecosystems and in microbiomes of various organisms. Hot research topics in this field include e.g. the role of human microbiomes in human health and characterizing metal-tolerant microbial communities from mining waste waters for bioremediation purposes. By far, the lack of broad-range primers has prevented simultaneous analysis of eukaryotic (fungi, phytoplankton) and prokaryotic (bacteria, archaea) members of microbial communities by amplicon sequencing.

The primer-independent RNA sequencing method developed by Mäki and Tiirola (2018) is more precise and cost-efficient than the traditional marker gene (16S rRNA) methods and can more easily provide a broader view of microbial communities (bacteria, fungi, phytoplankton). This method has high potential to be widely used method in the future.

Aim: The aim of the course is to widen understanding on RNA sequencing by introducing a new cutting-edge molecular method and provide practical skills for analyzing microbiological samples with primer-independent method.

Course lecturers: developers of the primer-independent RNA method, professor Marja Tiirola (Environmental microbiology, JYU) and researcher Anita Mäki (JYU). Professor Tiirola’s research group studies microbial processes and develops new tools for the high-throughput sequencing to characterize the functional role of microbes. Prof. Tiirola has over 60 peer-reviewed articles, cited over 2000 times (https://www.jyu.fi/science/en/bioenv/staff-and-administration/staff/tiirola-marja). Anita Mäki has wide experience on molecular laboratory analysis and methods and has had key role in developing the method in question (http://users.jyu.fi/~seanruus/).

Target group: The course is aimed for ten doctoral students and postdoctoral researchers in the fields of natural sciences and technology and health and biosciences. Participants should have basic knowledge, practical skills and some experience in working in a molecular laboratory.

Language: English

Contents: Lectures and practical laboratory work. Short presentation of your current research (5-10 min per student).

Course material: Mäki, A., & Tiirola, M. (2018). Directional high-throughput sequencing of RNAs without gene-specific primers. BioTechniques, 65 (4), 219-223. doi:10.2144/btn-2018-0082.

Program

Tuesday 20 August
12.15-16.00 Lectures (Place BF119-1)

Wednesday 21 August
09.15-11.00 Lectures and instructions (Place B132)
12.00-17.15 Laboratory work (Place B132)

17.30-19.00 Short presentations (snacks & refreshments; place to be announced later)

Thursday 22 August
09.15-11.00 Lectures and instructions (Place B132)
12.00-17.15 Laboratory work (Place B132)

19.00 ® Course dinner (own cost; place to be announced later)

Friday 23 August

09.15-11.00 Lectures and instructions (Place B132)
12.00-17.15 Laboratory work (Place B132)

Changes are possible

Note 1:

Full participation in each session is required.

Note 2:

More information about the course and registration before 20th June by email to Kaisa Lehosmaa (kaisa.lehosmaa [at] oulu.fi). A short motivation letter attached with your registration is mandatory. Since the number of participants is strictly limited registration is binding.

 

Last updated: 16.4.2019