What is this project?
This project is a web application, developed by Anjali Chawla and Malosree Maitra from the labs of Dr. Turecki and Dr. Nagy, for the interactive visualization of ATAC and single-cell RNA sequencing data. This project was supported by the inaugural competition of the Douglas Open Science Awards, in 2022.
This web application aims to facilitate the understanding of brain cell-type specific contributions to the healthy brain and their role in depression and suicide. A second open dataset now allows researchers to explore data on the expression of a gene and combine it with data on the accessibility of the associated chromatin region, gene promoter, and transcription factor motifs.
The application is open and accessible at no cost: scientists worldwide can use the data shared by the McGill Group for Suicide Studies (MGSS) to explore cell-type specific gene regulation and expression in individuals with depression who died by suicide compared with psychiatrically healthy controls.
Why single-cell sequencing ?
Single-cell sequencing allows for characterizing specialized cell types in different brain regions, including in the context of brain-related pathologies.
How is the application interactive ?
You can change the dropdown tabs to select variables of interest, compare samples side by side and download a PDF or PDG of created images.
How does the application promote open science?
The web application is an open-source software that makes data findable, accessible, interpretable and reusable (FAIR). It follows Douglas Open Science principles by:
- Facilitating data reuse, which contributes to research reproducibility and replicability;
- Allowing collaborations based on the shared data, contributing to knowledge dissemination and sharing.
Refrences
Chawla A., Cakmakci D., Zhang W., Maitra M., Rahimian R., Mitsuhashi H., et al. Differential chromatin architecture and risk variants in deep layer excitatory neurons and grey matter microglia contribute to major depressive disorder bioRxiv 2023.10.02.560567, (2023) doi: 10.1101/2023.10.02.560567
Maitra M., Mitsuhashi H., Rahimian R., Chawla A., et al. Cell type specific transcriptomic differences in depression show similar patterns between males and females but implicate distinct cell types and genes Nature Communications 14 (2912), (2023) doi: 10.1038/s41467-023-38530-5