Educational guide

IDENTIFYING DATA

2024_25

Subject

TRANSCRIPTOMICS AND FUNCTIONAL ANALYSIS

Code

01745012

Study programme

1745 - Máster Universitario en Investigación en Biotecnología y Biomedicina

Descriptors

Credit.

Type

Year

Period

Optional

First

Second

Language

Castellano

Prerequisites

Department

PRODUCCION ANIMAL

Coordinador

SUAREZ VEGA, AROA

E-mail

asuav@unileon.es
bgutg@unileon.es
mmarm@unileon.es
arodg@unileon.es
jgutg@unileon.es

Lecturers

GUTIÉRREZ GIL , BEATRIZ

MARQUÉS MARTÍNEZ , MARGARITA

RODRÍGUEZ GARCÍA , ANTONIO

GUTIERREZ GONZALEZ , JUAN JOSE

SUAREZ VEGA, AROA

Web

http://

General description

Tribunales de Revisión

Tribunal titular
Cargo	Departamento	Profesor
Presidente	PRODUCCION ANIMAL	ARRANZ SANTOS , JUAN JOSE
Secretario	BIOLOGIA MOLECULAR	GARCIA GARCIA , PEDRO
Vocal	PRODUCCION ANIMAL	BAYON GONZALEZ , YOLANDA

Tribunal suplente
Cargo	Departamento	Profesor
Presidente	BIOLOGIA MOLECULAR	SAENZ DE MIERA CARNICER , LUIS ENRIQUE
Secretario	PRODUCCION ANIMAL	SARO HIGUERA , CRISTINA
Vocal	BIOLOGIA MOLECULAR	GONZALEZ CORDERO , ANA ISABEL

Competencies

Type A	Code	Competences Specific
	A18951
	A18952
	A18954
	A18955
Type B	Code	Competences Transversal
	B5753
	B5754
	B5755
	B5756
	B5757
	B5758
	B5759
	B5760
	B5761
	B5762
	B5763
	B5764
	B5765
	B5766
	B5767
	B5768
Type C	Code	Competences Nuclear
	C1
	C2
	C3
	C4
	C5

Learning aims

	Competences
Perform and interpret differential gene expression analysis and identification of novel transcripts, including long non-coding transcripts, from massively parallel RNA sequencing (RNA-Seq) data.	A18951 A18952 A18954 A18955	B5754 B5757 B5758 B5759 B5760 B5761 B5764 B5766 B5767 B5768	C1 C2 C4 C5
Understand the theory of how functional enrichment tools produce statistically enriched functions or interactions.	A18952 A18954	B5753 B5755 B5757 B5758 B5761 B5764 B5766 B5767	C2 C3 C4 C5
Development of bioinformatics skills through the use of various programming languages.	A18951 A18954 A18955	B5754 B5755 B5758 B5761 B5763 B5766 B5767	C2 C4 C5
To acquire a deeper understanding of the biological and molecular basis of complex traits of interest in various organisms by performing and interpreting functional analyses.	A18951 A18954	B5754 B5755 B5756 B5758 B5762 B5764 B5765 B5766 B5767	C2 C3 C5

Contents

Topic	Sub-topic
I. Introduction	Topic 1. Introduction to transcriptomics Topic 2. Basic aspects for the design of an experiment and applications of RNA-Seq methodology. Topic 3. Introduction to programming languages: Linux and R environment.
II. RNA-Seq bioinformatic workflow	Topic 4. RNA-Seq Data Quality Control Topic 5. Mapping RNA-Seq data against the reference genome Topic 6. Sequence manipulation and visualisation with IGV Topic 7: RNA-Seq data assembly, types and applications Topic 8: Quantification and differential expression analysis. Topic 9: Time series analysis. Detection and annotation of mRNA and pRNA transcripts in prokaryotes: dRNA-seq, Term-seq.
III. Functional analyses and Systems biology	Topic 10: Principles of functional annotation, databases and functional enrichment analysis Topic 11: Functional Genomics and CRISPR/Cas9 Systems Topic 12: Meta-analysis and Introduction to Systems Biology

Planning

Methodologies :: Tests
	Class hours	Hours outside the classroom	Total hours
Practicals using information and communication technologies (ICTs) in computer rooms	19	28.5	47.5

Personal tuition	3	4.5	7.5

Lecture	8	12	20

Practical tests	0	0	0

(*)The information in the planning table is for guidance only and does not take into account the heterogeneity of the students.

Methodologies

Methodologies ::

	Description
Practicals using information and communication technologies (ICTs) in computer rooms	Presential practical sessions. Experimental trials, problems or computer simulations. Students will carry out or follow an experimental protocol following good laboratory practice, the guide to good practice in the handling of experimental animals and/or genetically manipulated microorganisms. In these sessions, the results obtained will be discussed by the students and the lecturer, analysing their importance and interest.
Personal tuition	Personalised assistance to the student. The student will be guided in self-learning activities. Analysis of relevant scientific articles on current topics related to the subject. - Preparation of written reports, oral presentations or seminars on experimental or bibliographical work. - Carrying out autonomous tasks online or in a computer classroom. Students will be able to attend during the lecturers' tutorial timetables. It is recommended to make an appointment by e-mail with the teacher. Tutorships may be held by email in case of impossibility of face-to-face tutoring.
Lecture	Presentation or discussion of the contents of the subject.

Personalized attention

Description

Assessment

	Description	Qualification
Practicals using information and communication technologies (ICTs) in computer rooms	Attendance at laboratory practicals (attendance and active participation in all training activities). 20% of the final grade Submission of the practical report. 30% of the final grade	50
Others	Assessment of the use of bioinformatics bioinformatics tools related to and capacity to interpret and discuss the results 50% of the final grade	50

Other comments and second call
Those tests not passed in the continuous assessment must be passed in the second ordinary exam. Final exam of the subject. The grading system will be in accordance with the stipulations of RD 1125/2003. Maximum weighting 70%.

Sources of information

Access to Recommended Bibliography in the Catalog ULE

Basic	Christina Marshall, Bioinformatics and Functional Genomics, CALLISTO REFERENCE, Dan MacLean, R Bioinformatics Cookbook: Use R and Bioconductor to perform RNAseq, genomics, data visualization, and bioinformatic analysis, Packt Publishing, Eija Korpelainen, Jarno Tuimala, Panu Somervuo, Mikael Huss, Garry Wong, RNA-seq Data Analysis: A Practical Approach, Chapman and Hall/CRC, Haja N. Kadarmideen, Systems Biology in Animal Production and Health, Vol. 1, Springer International Publishing,

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