Overview
This repository contains the analysis of seven single-cell RNA sequencing (scRNA-seq) in vitro samples of sonic hedgehog medulloblastoma (SHH-MB) cells and non-malignant human iPSC-derived cerebellar organoids. These samples represent a comparative study involving two distinct SHH-MB cell lines: DAOY and ONS-76. For each cell line, the cells were grown under various conditions:
- Monolayer
- Tumour spheroid
- Co-culture of tumour spheroid with non-malignant cerebellar organoid
- Control non-malignant cerebellar organoid
The purpose of this analysis is to uncover the cellular and molecular dynamics of SHH-MB under different growth conditions, contributing to our understanding of its pathobiology and potential therapeutic targets.
Contents
The PrePrint folder includes:
Analysis Notebooks: .Rmd files detailing the data processing, analysis, and visualization steps.
The root directory houses earlier iterations of analysis scripts. These .Rmd files are precursors to those found in the PrePrint/ folder and serve as a developmental record.
Getting Started
To replicate the analysis or explore the datasets, please ensure you have R and the necessary packages installed. The primary analysis is conducted in R Markdown documents, which can be rendered to produce comprehensive reports.
Clone the repository to your local machine. Navigate to the PrePrint folder. Open the R Markdown files in RStudio to execute or modify the analysis.
Data Availability
Due to the nature of this research, data used in this analysis may be subject to initial access restrictions. scRNA-seq data have been deposited in the National Centre for Biotechnology Information Gene Expression Omnibus (GEO) database and are publicly accessible through GEO accession number GSE254917 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE254917)
Citation
If you use the contents of this repository in your research, please cite as follows:
Analysis conducted by John Jacob, University of Oxford. Further citation details pending publication.