CG080 Methods in genomics

Faculty of Science
Spring 2025
Extent and Intensity
2/0/0. 2 credit(s) (plus 2 credits for an exam). Type of Completion: zk (examination).
In-person direct teaching
Teacher(s)
prof. RNDr. Jiří Fajkus, CSc. (lecturer)
Mgr. Petr Fajkus, Ph.D. (lecturer)
doc. Mgr. Miloslava Fojtová, CSc. (lecturer)
Mgr. Vratislav Peška, Ph.D. (lecturer), prof. RNDr. Jiří Fajkus, CSc. (deputy)
doc. Mgr. Petra Procházková Schrumpfová, Ph.D. (lecturer)
Mgr. Markéta Žďárská, Ph.D. (lecturer)
Guaranteed by
doc. Mgr. Miloslava Fojtová, CSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jiří Fajkus, CSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 17. 2. to Sat 24. 5. Tue 9:00–10:50 C02/211
Prerequisites
basic knowledge of analytical chemistry, biochemistry and molecular biology
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
major goal of this subject is to acquaint students overall and generally with methods used in genomics.
Learning outcomes
at the end of the course students should be able:
to explain principles of basic methods of genomic analysis
to propose appropriate methods for analysis of given sample type with respect to purpose of analysis.
Syllabus
  • • Nucleic acids isolation (gDNA, mtDNA, chlDNA, plasmid DNA, total RNA, mRNA). NA purification from aminal, plant and bacterial cells. Experimental design (buffers and detergents, inhibitors of nucleases, NA precipitation). Measurement of concentration, QC.
  • • NA separation techniques. Electrophoresis – types, experimental design, detection of DNA and RNA in the gel. The effect of DNA conformation on the electrophoretic separation.
  • • Cloning – restriction endonucleases, vectors. Cloning using plasmids, Gateway cloning, Golden Gate assembly.
  • • PCR – principle, history. Quantitative (real-time) PCR – principle, qPCR types (sequence-specific, sequence non-specific; absolute quantification, relative quantification; digital PCR). Application.
  • • Gene editing and chromosome engineering (ZFN, TALEN, CRISPR/Cas) – principles, application.
  • • Mutants and their utilization in genomics: Basic approaches of functional genomics, reverse and forward genetics. Insertional mutagenesis in forward and reverse genetics, EMS mutagenesis, identification of mutated loci via map-based cloning and NGS. EMS mutagenesis in reverse genetics – tilling.
  • • Sequencing, analysis of gene expression - principles of the chemical and Sanger sequencing, automatic capillary sequencing machines, next-generation sequencing.
  • • Preparation of NGS libraries for genome and transcriptome sequencing. Processing of the entry material according to the purpose of the analysis (rRNA depletion, poly-A mRNA selection). Quality control.
  • • Guide to raw NGS data processing (data transfer, storage, and quality control). Selected bioinformatic tools for different types of experimental data (whole-genome, transcriptome, metagenome data). Data upload to publicly available databases.
  • • Examples of NGS data processing in basic research: Working with local and distant type computational resources, e.g., GALAXY within the Virtual Organization METACENTRUM. Preparation of datasets for analysis. Bioinformatic tools for mapping and assembling. Special tools for repetitive component analysis.
  • • Methods of epigenomics – analysis of DNA methylation, histone modifications, chromatin structure.
  • • RNA structure, epitranscriptomics.
  • • Single-cell genomics, spatial genomics.
Literature
    recommended literature
  • Evolutionary genomics and systems biology. Edited by Gustavo Caetano-Anolles. Hoboken, N.J.: Wiley-Blackwell, 2010, xix, 465 p. ISBN 0470195142. info
  • PEVSNER, Jonathan. Bioinformatics and functional genomics. 2nd ed. Hoboken, N.J.: Wiley-Blackwell, 2009, xxviii, 95. ISBN 9780470085851. info
  • BUDINSKA, Eva, Otakar FOJT and Ladislav DUŠEK. Bioinformatics in Genomics and Proteomics Data. 2009. URL info
  • Biotechnology and genomics. Edited by P. K. Gupta. 1st ed. Meerut, India: Rastogi Publications, 2009, 796 p. ISBN 9788171338450. info
  • CAMPBELL, A. Malcolm and Laurie J. HEYER. Discovering genomics, proteomics, and bioinformatics. 2. ed. San Francisco: CSHL Press, 2007, xv, 447. ISBN 0805382194. info
  • Genomics. Edited by Isidore Rigoutsos - G. Stephanopoulos. New York: Oxford University Press, 2007, xxi, 314 p. ISBN 9780195300819. info
  • Functional genomics : methods and protocols. Edited by Michael J. Brownstein - Arkady B. Khodursky. Totowa, N.J.: Humana Press, 2003, xii, 258. ISBN 1588292916. info
  • Comparative genomics : empirical and analytical approches to gene order dynamics, map alignment and the evolution of gene families. Edited by David Sankoff - J. H. Nadeau. 1st ed. Dordrecht: Kluwer Academic Publishers, 2000, xiii, 557. ISBN 0792365844. info
  • Functional genomics : a practical approach. Edited by Stephen P. Hunt - Rick Livesey. 1st ed. Oxford: Oxford University Press, 2000, xviii, 253. ISBN 9780199637744. info
Teaching methods
The lecture is based on ppt presentations and their explication. Presentations themselves will be available as study materials (black-and-white printable pdf with high resolution and restricted access rights). It is recommended to attend the lecture, because of the explication, which significantly extends the presentation and because there are no available textbooks in Czech language covering certain parts of the subject. Students will test their acquired knowledge by means of "in-rough" tests, which will have similar form and content as the final examination test, they will be corrected to give the feed-back, but not graded.
Assessment methods
written & oral examination; multiple-choice test consists of sixty questions with four choices per question with always at least one correct answer. to pass the test, it is necessary to answer correctly at least 60 % of the questions; test covers complete content of the course. the examination will be finished by oral examination.
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Spring 2011 - only for the accreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024.
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