Formation - ChIP-seq, RNA-seq and Hi-C: treatment, analysis and data visualization

Scientific and technical environment of the training course

Institut de génétique moléculaire de Montpellier

- UMR 5535

COURSE DIRECTORS

Jean-Christophe ANDRAU

Senior researcher

UMR 5535

Amal MAKRINI

Research engineer

UMR 5535

Cyril ESNAULT

Researcher

UMR 5535

LOCATION

MONTPELLIER (34)

ORGANISATION

4,5 days: from Monday 08:45 a.m. to Friday 12:30 p.m.
Training course in English
From 8 to 12 attendees

PEDAGOGICAL METHODS

Lectures (5h) and practical courses (27h) supervised by 1 teacher for 4 attendees.
Along the course, corrected exercises will allow the attendees to evaluate their knowledge acquisition.
Paper support, files in PDF format and a Linux virtual machine will be made available to the trainee.

TRAINING FEES

1950 Euros

AT THE END OF THE TRAINING COURSE

- Satisfaction survey from trainees
- A training certificate is delivered

COURSE DATE

Nous consulter

2024

January	February	March	April
May	June	July	August
Sept	Oct	Nov	Déc 24027

OBJECTIVES

Learn how to plan a simple experiment of ChIP-seq or RNA-seq

Acquire the skills to evaluate data quality for transcriptome and gene regulation experiments

Understand and apply the principal methods and analysis tools for RNA-seq and ChIP-seq

Be able to visualize data in a genome browser and extract enriched regions

Learn how to manipulate and annotate enriched regions files using bedtools

Become acquainted with the principal methods of analysis for long-distance genomic interactions (Hi-C) and generate chromosomal interaction maps

PUBLICS

Engineers and researchers in biology
Pre-requirement : knowledge of basic command lines under Linux can be useful but not mandatory. A recall of basic knowledge will be proposed.

TRAINING PROGRAMME

Day 1: ChIP-seq and RNA-seq data pre-processing
- Initiation to Linux command lines (3 h)
- Basic notions of ChIP-seq, RNA-seq and Hi-C and their analysis pipeline, principle of spike-in normalization
- Pre-treatment of data (quality of raw data, alignments, sequencing artifacts)
- Exploration of aligned data (fragments size estimation, alignment quality)

Days 2 and 3: ChIP-seq analysis
- Generation of signal files (.wig) using the R-PASHA package
- Visualization of .wig files and isolation of enriched regions adapting detection parameters (MACS2 or using a genome browser option)
- Initiation to meta-profiling around regions of interest (genes, TSS, TES, enhancers)
- Enrichment of functional annotations (gene ontology)
- Motif search in enriched regions
- External spike-in normalization

Day 4: RNA-seq analysis
- Quantification of gene expression in RNA-seq data (RPKM)
- Spike-in normalization principle
- Differential gene expression analysis for transcripts and exons

Day 5: Hi-C analysis
- Quality controls, alignment and filtering of Hi-C data
- Generation of a chromosomal interaction map
- Visualization and interpretation of the interaction matrix
- Identification of subnuclear compartments
- Identification of Topologically Associating Domains (TADs) and loops
- Presentation of few databases and visualization tools for Hi-C
- Discussion (1 h) around participants questions and own problematics

EQUIPMENT

Each participant will access a working station under Linux with pre-installed softwares required for the training.

Avis des stagiaires

"Très bons support pédagogiques. Très bonne équipe de formateurs." Thierry J., Institut de recherche

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