Omics Techniques

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Credits
6
Types
Compulsory
Requirements
This subject has not requirements, but it has got previous capacities
Department
UAB
The aim of this course is to provide a basic vision of the application of Omic Techniques in different fields with the description of practical examples. The different themes that will be taught include recent advances in sequencing, epigenomics, metagenomics, single-cell genomics, advanced transcriptomic technologies, or proteomics. Maximum priority will be given to the application of the topics introduced in the lectures in different scientific areas, providing a basic training in a broad range of omic techniques. Given the current importance of this field, which is very dynamic and in permanent change, the scope and contents of the course will be subjected to regular updates.

Teachers

Person in charge

  • Jaime Martinez Urtaza ( )

Weekly hours

Theory
2
Problems
2
Laboratory
0
Guided learning
0
Autonomous learning
6

Objectives

  1. Acquisition of specific knowledge to apply the different technologies and strategies to generate sequencing data (DNA and RNA)
    Related competences: K1, K7, S1, S2, C2, C3,
  2. Application of genomic, transcriptomic and proteomic data within different contexts to solve biological problems
    Related competences: K1, K2, K3, K7, S2, S3, S7, S8, C2, C4,
  3. Understand the experimental and computational methods of genomics, transcriptomics and proteomics
    Related competences: K1, K2, K3, K7, S1, S2, S3, S5, C2, C4,

Contents

  1. Sequencing technologies
    Generation of sequencing data. Sanger sequencing; 2nd and 3rd generation sequencing techniques (Illumina, Oxford-Nanopore, PacBio).
  2. Applications of DNA-seq
    Sequencing and processing of DNA sequencing data: genome sequencing, re-sequencing and variant calling.
  3. Metagenomics and microbiome
    Applications of metagenomic and microbiome analysis; pipelines and data analysis to study natural environments and health.
  4. RNA sequencing and analysis of RNA-seq data.
    Analysis of RNA-seq data to understand gene expression and its variations across different conditions: quality control, read alignment, quantification, and differential expression analysis.
  5. Applications of RNA-seq
    Gene expression and splicing variant annotation, metatranscriptomics. Applications in different fields: disease diagnosis, drug discovery, and functional genomics.
  6. Epigenomics and epigenetics
    Epigenomics and epigenetic modifications on the genetic material: data processing and analyses for differential DNA methylation.
  7. Hi-C for 3D genome organization.
    The study the three-dimensional structure of genomes to understand how the spatial organization of DNA influences gene expression and other cellular processes. Hi-C protocols and general processing of Hi-C data.
  8. Single-cell genomics.
    Study of the genetic material (genome, transcriptome) of individual cells: applications and analysis.
  9. Proteomics.
    Methodological foundations of the techniques to study of the protein composition (proteome) within a cell or organism. Special emphasis will be placed on the technologies developed for protein identification, including mass spectrometry and DIGE technology, and their applications in biomedicine.

Activities

Activity Evaluation act




Teaching methodology

- Theoretical classes. Lectures will address the main concepts behind the different topics. They will consist of question-based lectures that promote an active participation of all students in the discussion of different topics/situations/problems/cases that will be presented.

- Practicals. Hands-on problem-based tutorials. They will promote both self-study and teamwork learning strategies. Please bring your laptop computers in class.

Evaluation methodology

The success in meeting the course learning objectives will be evaluated as follows:

- Continuous assessment (40%): may include tests of combined multiple-choice and/or short-answer questions to recapitulate worked contents in each unit, homework, programming exercises, group activities proposed in class, etc.

- Exam (60%) consists of a 2 partial theoretical-practical exams taken at mid term (30%) and final term (30%).

Overall, in order to successfully complete this course, the student must get a minimum final grade of 5 points (out of 10).

Make-up exam: only the students that after the regular evaluation have not passed the course can take a reassessment exam. The grade obtained at the make-up exam will substitute the failed regular grade obtained during the trimester.

Bibliography

Basic:

Web links

Previous capacities

NA