Hello,
I was looking at the expression of CCR2 in the whole mouse brain scRNAseq data set. Visually looking at expression, most of the cells analyzed are a light yellow, indicating on the logarithmic histogram that the overwhelming majority of cells show some low-level expression of CCR2. However, when I go to select a subset of these cells to download, there are “No cells selected,” which makes me question if I am reading the coloration incorrectly for the expression of CCR2; perhaps these cells do not express any CCR2? This would make sense with what the data says when organized by clusters, in that most cell clusters in the brain seem to not express any CCR2; however, that does not seem to be indicated as a possibility on the histogram of CCR2 expression. Can someone please help me figure out what the RNA expression of CCR2 is in the mouse brain? Are there cells in the brain that do not express any CCR2?
Thanks!
Hello,
Based on the light yellow coloring, it sounds like you are using the ABC Atlas (which shows low expression as yellow and high expression as dark purple). If you are not using the ABC Atlas, please let me know which tool you are using.
I opened up the ABC Atlas, and on the lefthand UMAP I have the plot colored by CCR2, and the righthand UMAP is colored by cell classes. Based on these plots, it looks like almost all of the CCR2 expression is restricted to immune cells (the small brown island in the upper left corner of the righthand UMAP, you can see “immune cells” by hovering your mouse over the island). To find more information about the cells with high CCR2 expression, you can use the selection tool (the dashed square in the upper right corner of the UMAPs) to select a group of cells. After selecting the high expression CCR2 island, a “Selected cells” panel pops up on the right which gives me ranges of CCR2 expression values and cell type annotations for the selected cells.
You can view these two UMAPS here: Brain Knowledge Platform
This image shows the selection tool in use:
