This repository contains code for the manuscript: Integration of human and mouse single-cell transcriptomes of the developing cerebellum identifies potential cell-of-origin for Group 3 and 4 medulloblastoma

Ian Cheong, Leo Lau, Shraddha Pai

bioRXiv preprint link TBA

Preparation of input datasets

See scrnaseq_Leo/integrations/pipeline_instructions.txt for steps. Code to standardize processing of each input dataset is in: scrnaseq_Leo/dataset_processing

Human-mouse integration

• The pipeline to perform integrations is in scrnaseq_Leo/integrations. See pipeline_instructions.txt.
• UMAP of resulting integration: manuscript_output/figures/results/integ_full.qmd
• Visual comparison of different integration methods: manuscript_output/figures/results/integ_methods.qmd
• Assignment of labels to cell clusters: software/utilities/cell_labeling.R
• Subsetting of rhombic lip cells and non-neuronal reference cells: scrnaseq_Leo/notebook/notes/_20240524.qmd
• Plotting UMAP, cluster markers of integrated rhombic lip cells: manuscript_output/figures/results/rl_gene_expr.qmd and integ_rl.qmd
• Proportion tests for rhombic lip: lab_notebook/notes/_20240822.qmd and lab_notebook/notes/_20240823.qmd

Subclustering of UBC and plots

• Subsetting for UBC: lab_notebook/notes/_20240825.qmd
• Finding and plotting best clustering resolution: manuscript_output/figures/results/ubc_cluster_res.qmd
• Plotting UMAP and proportion tests: manuscript_output/figures/results/ubc_cluster_res.qmd
• scProportionTest calculate: scrnaseq_leo/notebook/notes/_20240718.qmd
• Propeller calculate: scrnaseq_leo/notebook/notes/_20240606.qmd
• DEG analysis: scrnaseq_leo/notebook/notes/_20240715.qmd
• Pathway analysis: lab_notebook/notes/_20241029.qmd
• PySCENIC: lab_notebook/notes/_20240704.qmd
• Plots of DEG in UBC clusters and top regulons: manuscript_output/figures/results/ubc_genes_regulons.qmd
• Pseudotime calculation: lab_notebook/notes/_20240611.qmd
• Pseudotime plots: manuscript_output/figures/results/pseudotime.qmd
• Plot cluster distribution by sex: manuscript_output/figures/results/plot_ubc_sexdistr.qmd

Integration with tumours

• QC & testing multiple integration methods for tumours, inc. FastMNN: lab_notebook/notes/_20230510.qmd
• Plotting tumour UMAP, Group 4 MB tumour volcano plot, intersection of TFs in Group 4 MB and UBC 1, and top regulons: manuscript_output/figures/results/mb_similarity.qmd
• DEG analysis: lab_notebook/notes/_20240827.qmd
• PySCENIC: lab_notebook/notes/_20240928.qmd
• Projection of developmental cell states: manuscript_output/figures/results/annot_cluster_single_IanUBCs.R