The ChIP-seq and BigData workshops

125 heures / 12 ECTS

 
Dual skills training
2 practical workshops
ChIP-seq workshop
(1 week)

​The ChIP-seq is a molecular biology technique that allows the genome-wide study of DNA/protein interactions. It combines the immunoprecipitation of a protein of interest with the high-throughput sequencing of co-precipitated DNA fragments.​

This is a hands-on practical workshop. Each pair of attendees will do a chromatin immuno-precipitation:

  • Crosslink of the material

  • Extraction and fragmentation of the chromatin

  • Check the sheared chromatin on gel

  • Immunoprecipitation (of histone post-translational modifications or RNA polymerase)

  • Purify immunoprecipitated DNA

  • Validate ChIP enrichment by qPCR

Illumina sequencing of the immunoprecipitated DNA

  • Sequencing banks will be prepared using IPed DNA with proper enrichment and yields.

Big Data workshop
(3 weeks)

The Big Data workshop is dedicated to biology and medicine students who wants to acquire skills in NGS data manipulation, treatment and statical analysis.


This training is for beginners, no previous training in computer required.

Through this workshop, students will gain the basics of manipulation, processing, and statistical testing to independently analyze high-throughput sequencing data.

 During this course, students will be able to:

  • Describe the experimental techniques to achieve ChIP-seq experiments

  • Manipulate high-throughput sequencing files. Choose, set parameters for, and execute software packages for data analysis. Perform sequence alignments, filtering, normalization and quality control.

  • Master the different steps of the differential analysis of RNA-Seq data to sort out differentially expressed genes.

  • Analyse ChIp-Seq data and perform peak-calling

  •  Computerize and concatenate bioinformatics tools to create workflows

  •  Choose the apropriate statiscal model and the R package to analyse and correlate the data sets, according to their structure

  •  Execute clustering of the data (hierarchical clustering, PCA...)

  •  Analyze and interpret the experimental results, formulate conclusions or hypotheses from these data. Discuss biases, limitations and errors 

  • Choose the appropriate graphs, and draw figures to visualize high-throughput data

Les  résultats de ChIP-seq seront analysés lors de l'atelier BigData

Visit of sequencing platforms of
I2BC and Genoscope

The Institute for Integrative Biology of the Cell (I2BC) 

I2BC_Logo_modifié.jpg

Genoscope - National Center of Sequencing