This repository contains code used to process and analyze two scRNA-seq datasets prepared from co-culture and organoid models of Alexander disease. Samples were processed using the 10X Genomics platform. The data have been deposited in Gene Expression Omnibus under accession number GSE261158. In August 2024, the code has been updated with changes related to revision of the related manuscript. Aberrant neurodevelopment in human iPS cell-derived models of Alexander disease is now published in Glia journal at: https://onlinelibrary.wiley.com/doi/full/10.1002/glia.24618.
The repository includes the following folders and files:
samples.csv
- information about samples which was used in preprocessing
2017_07_preprocessing.R
- fastq_screen
- STAR alignment
20211222_scRNA_preprocessing.Rmd
- EmptyDrops - filtering of empty droplets
- quality control
- integration
- initial clustering and annotation
- identification of low-quality cells
- DoubletFinder
20211230_scRNA_analysis.Rmd
- more accurate annotation
- subsetting to cell populations
- velocyto, monocle
20220221_coculture_AxD_code.Rmd
- identification of contamination with SoupX and repeated analysis of corrected data including quality control
- clustering, subclustering, and annotation
20220307_scRNA_post_SoupX.Rmd
- Cerebro
- additional quality control and finalized annotation of clusters
20220225_DEA.Rmd
- identification of differentially expressed genes
- Gene Ontology enrichment analysis
20230216_CellChat.Rmd
- CellChat analysis of cell-cell interaction patterns
20221006_coculture_figures.Rmd
- code used to generate all figures that are in the manuscript
samples.csv
- information about samples which was used in preprocessing
2017_07_preprocessing.R
- fastq_screen
- STAR alignment
scRNA_analysis.Rmd
- Seurat analysis
- integration
- quality control
- clustering
- annotation
- comparison of RNAseq and proteomics data
- code used to generate figures in the manuscript
DEA.R
- differential expression analysis
- Gene Ontology enrichment analysis
RTqPCR_plots.R
- code used to generate RT-qPCR plots
Gruffi_stress.Rmd
- Gruffi tool used to identify stressed cells in organoids
CellChat.Rmd
- CellChat analysis of cell-cell interaction patterns
overlap_with_coculture.R
- code used to compare co-culture and organoid datasets