Here is an overview of the different options for your epigenetics projects:

ChIPseq project:

The requesting team is responsible for preparing the immunoprecipitated DNA. GENOM'IC takes care of preparing the libraries using Diagenode's MicroPlex kit. We then perform paired-end sequencing with a number of reads adapted to the target you are studying (transcription factor, histone marks, etc.).

ATACseq project:

The requesting team can provide us with either isolated DNA fragments after tagmentation or pre-prepared libraries. The samples will be sequenced in paired-end mode with 50 million reads per sample.

CUT&Run or CUT&Tag project:

The team can provide us with previously isolated fragments or entrust us with libraries prepared by them. The samples will be sequenced in paired-end mode, with a number of reads varying from 2 to 10 million per sample.

Do you have questions about the strategy to adopt for your project? Feel free to contact us to discuss it!

Bioinformatic data analysis

We offer a comprehensive range of standard and advanced analyses, including:

•     Quality control of reads (FastQC, MultiQC).
•     Sequence alignment to the reference genome with Bowtie2.
•     Peak calling with MACS3.
•     Peak annotation by ChIPseeker (proximity to genes, regulatory regions, etc.).
•     Functional analysis (Gene Ontology, pathway enrichment) on request with clusterProfiler.
•     Differential peak analysis (comparison between conditions) with Diffbind.
•     Optional motif discovery.

Each project is discussed in advance with the facility to define the most appropriate experimental and bioinformatics strategy.

For all enquiries, please contact the platform at:

u1016-genomique@inserm.fr

What if our services do not cover your bioinformatics needs? You can contact the BIOINFORMAT'IC core facility at any time to discuss this!