Genomics and Transcricptomics

elective courses

For best understanding of the subject students should have the knowledge about the structure and function of nucleic acids in Prokaryotes and Eukaryotes.

Classroom

During the course students will be familiarized with the newest high-throughput technologies applied in the genomic and transcriptomic studies - on the experimental and bioinformatic level.

Through review of research articles the course will provide students an explanation of how these methods are applied in biology and medical science.

Practical problems emerging during experimental work-flow of DNA microarray analysis and next generation sequencing will be discussed.

Students will learn the newest technologies developed in the last decades, students will perform microarray experiment, prepare genomic libraries ready for NG sequencing and run the sequencing.

The aim of the course is also to provide students basic bioinformatical skills in genomics and transcriptomics.

The lectures will cover the following topics:

1.The history of research studies on the DNA and chromatin structure

2. The current definition of the gene and transcript; levels of transcription; an alternative splacing.

3. The basics of microarray technology and its application in transcriptomic and genomic analysis.

4. The development of DNA sequencing methods.

5. The principles of large-scale experiments design.

6. Genomic and transcriptomic data analysis.

7. Structure and function of the human genome - large-scale analysis.

9. Microarray analysis and Next Generation Sequencing (NGS) in medical diagnostics.

10. Epigenetic regulation during development.

11. NGS in species analysis.

12. Overview of large-scale phenotypic tests in model organisms.

13. The use of large-scale analysis in the study of human evolution.

14. Study of the population of microorganisms from the environment – application in metagenomics.

Laboratory.

Experiments will be performed by students themselves, working in pairs.

Topic 1. Microarray (Affymetrix - Gene 1.1 ST Array Strip) analysis of transcriptome changes in rat peripheral blood mononuclear cell (PBMC) after cardiac infarction.

RNA isolated from PBMC from rats after induced cardiac infarction and healthy (control) will be analyzed. Students will learn the method of RNA isolation from rat PBMC and perform analysis of RNA quality and quantity. Then RNA samples will be prepared for hybridization to Affymetrix Gene 1.1 ST Array. After hybridization 4 microarrays will be scanned using GeneAtlas system from Affymetrix.

The microarray data will be analyzed with Partek Genomic Suite software (Partek, Inc.). Students will learn about the basic functions of the software through statistical analysis of data obtained during experiments performed at the practical course. Students will also have a chance to analyze results of a scientific project of Department of Genetics, IBB, PAN.

Topic 2. Analysis of mechanisms and the role of some of core histone modyfications in regulation of transcription, through Next Generation Sequencing (NGS).

The goal of the course is to introduce next generation sequencing to students. The training will include all the steps necessary for preparing and validating DNA libraries for sequencing, as well as analysis of generated during the experiments data. Students will analyze immunoprecipitated plant DNA from Arabidopsis thaliana with antibodies against Polymerase II RNA and selected modified core histones. After checking the quality of input DNA with Bioanalyzer 2100, students will perform DNA library construction with the use of Illumina Library Prep Kit (Illumina). After validation on Bioanalyzer 2100 and qPCR, the libraries will be hybrydized onto a sequencing flow cell on cBOT machine (Illumina). Hybridized libraries will be sequenced on HiScanSQ system (Illumina), and the sequencing results will be analyzed in CASAVA software (Illumina) and visualized in Integrated Genome Browser software (BioViz).

Genomes. New Edition. TA Brown.

The lecture part will provide students knowledge about: eukaryotic genomes; chromatin structure; regulation of gene expression; the application of DNA microarray analysis and NG sequencing in research studies. Students will learn how to plan a correct high-throughput experiment for genomic studies.

Practical course will familiarize students with experimental work with DNA and RNA; individual laboratory work and using microarray and NGS systems. Students will gain experience in bioinformatic analysis of genomic data.

At the end of laboratory course students will take a written test with close-ended questions. Passing the test is necessary for taking the final examination.

The final exam will include both open and close-ended questions.