Functional genomic data analysis : epigenomics
Master in Life Science, ENS
UNBIO1-075 (E16) | Functional genomic data analysis : epigenomics
Year and Semester : M2 | S1
Where : Biology department, ENS
Duration : 1 week, 30 hours
Dates : September 16-20, 2024
Maximum class size : 18 students
Coordination
Morgane Thomas-Chollier, Biology Department, ENS (MC ENS)
Credits
3 ECTS
Keywords
Regulatory genomics | ChIP-seq | Bioinformatics | cis-regulatory elements | Motifs analysis.
Course prerequisites
• Enrollment to the course Functional genomic data analysis : trancriptomics. You need to enroll to this course as a pre-requisite, as it presents some introductory concepts (firsts steps of high-throughput sequencing data processing) and competencies in using the IFB computing infrastructure. Both are considered as previous knowledge for this teaching unit.
Competency level in Unix : Advanced exploration of the file system, and workspace. In addition, some competencies of levels 5 and 7 will be used ; these competencies will be learned during the transcriptomics course (see below).
Important : As this course is organised at the very beginning of the semester, enrollment for this course is considered as final early summer.
Course objectives and description
Aims : Mastering of concepts and software tools for the analysis of cis-regulatory sequences from ChIP-seq / ATAC-seq experiments. Practical experience of the analysis of high-throughput datasets. Develop a critical view on the dataset quality.
Themes : This teaching unit introduces the experimental approaches used for the detection of cis-regulatory elements in genomic sequences. It then focuses on ChIP-seq experiments. It covers the main bioinformatic and statistical concepts enabling the processing of raw data to obtain peaks, and then downstream analyses to extract meaningful biological information to answer the biological question initially asked. Discovery of motifs in ChIP-seq peaks for different transcription factors is also introduced.
To complement the lectures and practical hands-on sessions, seminars will be given by researchers, to highlight the biological and medical applications of ChIP-seq and the joint work between experimentalists and bioinformaticians, to present analyses taking into account the tridimensional organisation of the chromatin, and the analysis of variations in cis-regulatory elements.
Organization : The teaching unit will be organised over one week, with hands-on sessions, in addition to a practical project for which time is dedicated for personal work.
Assessment
A very short report on the practical project is due at the end of the week, to be written during the dedicated time for personal work.
Infrasctucture
The practicals will be conducted on the core cluster of the Institut Français de Bioinformatique. We kindly acknowledge the IFB for supporting this course.
