TP de Génomique (Polytech 4A)

The aim of this practical session is to provide students with the basic concepts and skills needed to perform ChIP-Seq experiments. During the session (~40h), the students will perform immunoprecipitation of nucleosomes displaying H3K4me3 and H3K4ac modification then sequencing of purified bound DNA.

Funding and acknowledgments

Note

We would like to thank all the people that were involved in the preparation of this practical session especially:

• Jean Imbert (TAGC/TGML/CoReBio PACA)
• Bertrand Jordan (CoReBio PACA)
• Beatrice Loriod (TAGC/TGML)
• Christian Reil (CoReBio PACA)
• Anne Chorazewiez (ex CoReBio PACA)
• Fabienne Thiry (Polytech)
• Myriam Ramadour (PGM)
• Sophie Gall (PGM).

We would like to gratefully acknowledge CoReBio Paca which provided us with the funding to set up this practical session.

Year

2014-2015

Attendees

9 students from Polytech Marseille.

Trainers

• Denis Puthier (TAGC)
• Lydie Pradel (TAGC)
• Nicolas Fernandez (TAGC/TGML)

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Contents:

• ChIP-Seq
• Library preparation
• Analysis of ChIP-Seq data produced during the practical session.
  • Setting up your working session
  • First step in creating a make file
  • The final makefile produced with the students

Datasets

Note that datasets are password-protected.

Dataset	FileName
H3K4me3 (NS)	H3K4me3-NS.zip
H3K4me3 (S)	H3K4me3-PMA.bw.zip
H3K27ac (NS)	H3K27Ac-NS.bw.zip
H3K27ac (NS, LV)	LV-K27Ac-NS.bw.zip
Summary (NS, S)	DataSummary.zip
Info (NS, S)	DataSummary_info.txt.zip

Note

The Summary file contains various information about transcripts expressed in the cell line. The info file describes each column.