The project was done by the team of four MSc Skoltech studetns: Alisa Fedorenko, Ekaterina Kashuk, Ksenia Kubenko, and Leonid Sidorov.
In this repository one can find the workflow for the final project of "Omics Data Analysis" course concerning the epigenome changes in mouse brain. Neuronal and glial cells demonstrate different pattern in chromatin structure (the difference can be found literally by eyes). The aim of the project is to elucidate changes in mouse epigenomic profile of neuronal and glial cell and try to use it for explanation of chromatin diversity.
Our goals:
- To compare neuronal and glial H3K9me3 track around the H3K27me3 regions in neurons, to investigate Ring1B (PRC1) linkage with H3K27me3 marks - Alisa Fedorenko;
- To detect significantly interacting regions (fithic) and to intersect it with H3K27me3 track, to identify H3K27ac track for open chromatin, to compare this track around the H3K27me3 - Leonid Sidorov;
- To find out a correlation between compartments, TADs and gene expression - Ksenia Kubenko;
- To explore chromatin difference in neuronal (NeuN+) and non-neuronal (NeuN−) nuclei (TADs density, loops prominence, compartment changes) - Ekaterina Kashuk.
All the datasets were taken from the materials of the following articles:
- Chandrasekaran S, Espeso-Gil S, Loh YE, Javidfar B et al. Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions. Nat Commun 2021 Dec 13;12(1):7243. PMID: 34903713
- Bonev B, Mendelson Cohen N, Szabo Q, Fritsch L et al. Multiscale 3D Genome Rewiring during Mouse Neural Development. Cell 2017 Oct 19;171(3):557-572.e24. PMID: 29053968
- Ximerakis M, Lipnick SL, Innes BT, Simmons SK et al. Single-cell transcriptomic profiling of the aging mouse brain. Nat Neurosci 2019 Oct;22(10):1696-1708. PMID: 31551601