Merfish gene panel

I’m wondering why the file (cl.df_CCN202307220.xls, tab- MERFISH GENE PANEL) posted under the link “Whole adult mouse brain taxonomy of cell types” only lists ~500 genes, when the Zhang et al paper mentions >1000, as does the “media-1.xls” file…? Is there something special about that subset?


this gene panel is probably the one used for the Allen dataset. We used a 500 gene panel, the max currently available for MERSCOPES).


Thanks very much!

I am still a bit confused… so is the Allen “MERFISH” atlas based on 500 or 1000 genes and how does this atlas relate to the Zhang et al., '23 Nature paper (the data availablity section refers one to the MERFISH atlas)? thanks for any insight

Maybe I need a clarification on what you mean by at last. Do you mean the spatial dataset of the entire taxonomy generated by clustering RNAseq data?
For the Allen MERFISH dataset we used a 500 gene panel to map each cell to a cluster form the RNAseq taxonomy. The Zhang et al. paper used a 1000 gene panel to map to the same RNAseq taxonomy.
The 500 genes we used are a subset of the 1000 genes used by Zhang et al. 23.
Let me know if that answers your question.

Yes, thank you very much… I realized that after re-reading the Yao paper. So I’m assuming that the 500 genes are enough to define the cell clusters defined by the scRNA seq in the Yao paper.