The Geographical Ecology group at Seoul National University (Web page: http://biosci.snu.ac.kr/homepage/professor/professor.php?homeid=geoecho ) is active in a range of research projects in community metagenomics of small organisms including bacteria, archaea, fungi, nematodes and mites.
We are interested in canvassing for interest in the possibility of workshops to teach practical aspects of community metagenomics for ecologists. Each workshop will consist of several days of morning lectures followed by afternoon lab-based tutorials. The workshops will be aimed at researchers (including professors, postdocs and graduate students) interested in using community metagenomics in their work. One workshop may be held at SNU in January 2014, another in June 2014. Sincerely, Jonathan Adams Here is a preliminary syllabus for the workshop: Proposal for training workshop Suggested attendees: 15-20 Fee per attendee: $800, or $150 per individual day. Lectures: Seminar room Lab tutorials: Teaching lab Metagenomics in Community Ecology: practical knowledge for environmental scientists. Aims: Metagenomics is one of the most rapidly advancing fields of biology. It has great promise for community ecology, where large numbers of small organisms are being sampled. This workshop will offer a series of lectures and step-by-step lab based tutorials on the techniques involved in metagenomic ecology. Lectures and tutorials will be conducted by experienced (3rd year) grad students and postdocs from the group of Prof. Jonathan Adams at SNU. Syllabus: Day 1: Morning Lecture: A brief introduction to community metagenomics in ecology. History, and examples of published studies. Lecture: Sampling for environmental DNA. Sampling strategies, handling and storage of samples. Legal aspects of transferring soils and biological samples. Lecture: Extracting DNA. DNA kits. Choosing the right DNA kit for your samples. Afternoon Lab based tutorial. Sampling of soil on campus followed by use of a soil DNA kit to extract and then purify DNA. Day 2. From extracted DNA to PCR. Morning Lecture: Assessing DNA quantity in an extracted sample Lecture: Use of PCR, use of qPCR, choices of amplicon regions, choices of primers. Lecture: Assessing the success of your PCR. Sources of problems with PCR. How much PCR product is enough? Afternoon Lab based tutorial, running PCR on a sample. Running a gel to assess results. Running qPCR on a sample. Taking results of qPCR. Day 3. Massively parallel sequencing Lecture: An introduction to popular platforms: 454, Illumina, HiSeq, MiSeq, ion torrent. Choice of companies for your sequencing. Lecture: Advantages and disadvantages of the various methods. Data output formats and how to read them. Lecture: Preparing your PCR product to send for sequencing. Best ways to store and send PCR product. Practical and legal issues of transferring PCR product. Afternoon Lab based tutorial: Preparing PCR product for sending. Drying PCR product. Downloading FASTA and other files of output. Opening and preliminary reading of output files. Day 4: Quality control of your sequencing output. Lecture: Sources of sequencing error and the importance of quality control. Lecture: Chimera checkers Lecture: Alignment of your sequences Lecture: Checking for frameshift errors in protein-expressing genes Afternoon Lab-based tutorial: Using a chimera checker, alignment of sequences, use of a frameshift checker. Day 5: Assignment of sequences to taxonomic categories Lecture: Online databases of sequences. Guidelines and limitations. Lecture: The OTU concept. Assigning your sequences to OTU’s. Placement relative to known taxonomic categories and other sequences in databases. Afternoon: Lab-based tutorial: Using an online sequence database, assigning your sequences to known categories. Day 6. Display and treatment of metagenomic community data Morning: Lecture: Plotting the results, indices of diversity. Community ordination Morning lab-based tutorial: plotting metagenetic output graphically, performing an ordination. Afternoon: Trip to Chunlab and MACROGEN labs.
