I recently used the RNA explorer (10x and SMART-seq) to view expression of the mechanosensitive channel Piezo1 which is known to be expressed in the motor cortex and hippocampus of mice. The heatmap results did not show expression except for a very minimal level in a single cell type. I’m curious as to why this protein did not show expression. Any suggestions?
I don’t have a good answer for why Piezo1 is not expressed in the Transcriptomics Explorer. It is worth noting that this gene IS expressed in the expected brain regions in the newer whole mouse brain atlas, which can be explored in the ABC Atlas. I would suggest using this tool for your use case.
My guess (emphasis on guess) is that it has something to do with how this particular gene is defined in the version of the transcriptome used for that data set. Another possibility is that this gene is highly expressed in a small fraction of genes across multiple types. Since we are showing trimmed mean, if the gene is expressed in <25% of genes of a given cluster it will show up as 0. Given the expression of Piezo1 in the ABC Atlas and original Mouse Brain ISH Atlas, I think this is less likely.