single-cell data object

shengqh / Hurley2022scRNA

Code for prostate cancer paper

MIT License

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single-cell data object #4

Closed cathalgking closed 1 year ago

cathalgking commented 1 year ago

I would like to use the single-cell RNA-seq data from this paper as a 'reference' for cell type label annotation. I see that the data is deposited on GEO but it only seems to be raw data or count matrices. Is there anywhere that I can get an R Seurat object (or python) single-cell object which includes the cell type labels? As shown in figure 1(i). Thanks

shengqh commented 1 year ago

The R object has been uploaded to GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185344.

https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE185344&format=file&file=GSE185344%5FPH%5FscRNA%2Efinal%2Erds%2Egz

cathalgking commented 1 year ago

I downloaded the object and loaded it into R. However, I don't see the cell type annotations in the R object (Mast cells, Myeloid cells, T cells etc.) as shown in Figure 1 of the paper. Where can I get this info?

shengqh commented 1 year ago

You can download the meta data from GEO:

https://ftp.ncbi.nlm.nih.gov/geo/series/GSE185nnn/GSE185344/suppl/GSE185344_PH_scRNA.rename_cluster.csv.gz