2024-12-28 - Benchmarking of Chromatin Immunoprecipitation (ChIP-Seq) methods in the Pacific oyster Magallana gigas
Published in bioRxiv, 2024
Recommended citation: Dellong, A., Fallet, M., Stenger, PL., Chaparro, C., Vidal-Dupiol, J., Clément, J., Cosseau, C. & Grunau, C. (2024). Benchmarking of Chromatin Immunoprecipitation (ChIP-Seq) methods in the Pacific oyster Magallana gigas. bioRxiv, 2024-12, https://doi.org/10.1101/2024.12.28.630603 https://www.biorxiv.org/content/10.1101/2024.12.28.630603.full.pdf
Abstract
Chromatin Immunoprecipitation sequencing (ChIP-seq) is the method of choice to generate chromatin landscapes across genomes. The scarcity of literature on ChIPseq and absence of a canonical “gold standard” method in mollusks and especially the pacific oyster Magallana gigas, prompted us to compare four ChIP-seq methodologies (Native-ChIP, Crosslink-ChIP, ChIPmentation and Cut & Tag) to find the most suitable method for this species. Our results show that Cut & Tag performs best and ChIPmentation worst. We hypothesize that the reason for this lies in a particularly fragile chromatin structure around genes in the oyster.
Recommended citation: ‘Dellong, A., Fallet, M., Stenger, PL., Chaparro, C., Vidal-Dupiol, J., Clément, J., Cosseau, C. & Grunau, C. (2024). Benchmarking of Chromatin Immunoprecipitation (ChIP-Seq) methods in the Pacific oyster Magallana gigas. bioRxiv, 2024-12, https://doi.org/10.1101/2024.12.28.630603’
