Re-analysis of snRNA-seq data from Schirmer et al., Nature, 2019.
This project aims to assess the gene expression of the colony stimulating factor 1 receptor (CSF1R) and its ligands, colony stimulation factor 1 (CSF1) and Interleukin 34 (IL34), in human (MS and control) samples. We utilized the single-nucleus RNA-sequencing (snRNA-seq) dataset from Schirmer et al. (Schirmer, L., Velmeshev, D., Holmqvist, S. et al. Neuronal vulnerability and multilineage diversity in multiple sclerosis. Nature 573, 75–82 (2019). https://doi.org/10.1038/s41586-019-1404-z). The raw fastq file were obtained from the NCBI Sequence Read Archive (SRA) under the accession number PRJNA544731 and analyzed with the Cell Ranger software (10x Genomics) to obtain an UMI per cell expression matrix.
Data analysis was done within the R environment using the Seurat package (Butler, A., Hoffman, P., Smibert, P. et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 36, 411–420 (2018). https://doi.org/10.1038/nbt.4096).