I am trying to do the single cell RNAseq of BBB specific cells, importantly the endothelial and mural cells from mouse stroke brain samples. I am finding it hard to decide whether I should isolate the micro vessels, dissociate them into single cells and use it or homogenize the entire brain hemisphere and get the single cells for the RNAseq? Can anyone let me know what would be the best approach?
This might be an approach for isolation of single cells, which can then be further processed using Bulk RNAseq:
https://www.nature.com/articles/s41596-023-00805-y.epdf?sharing_token=HZxtBBWvFH5FinxszdlO7dRgN0jAjWel9jnR3ZoTv0M3M4w9FY1Pf54Jgjy1O7o6fviaxAHgpM0eiVVb2_MwOK1IM0CTHhUCh83sS_qYPqVxW57yssZ5XauwO5-ngNYpvoCm2R5h4FAIeuQetvZd-WJIC7l0rvsWzqdjAWm5OPs%3D
Article Profiling the neurovascular unit unveils detrimental effects...
Perhaps have a look at publications from the Betsholtz lab (https://betsholtzlab.org/VascularSingleCells/database.html). These are the leading papers for mouse vascular RNAseq. Vessel isolation has been essential for sufficient numbers of vascular cells/nuclei from human brain. Yang...Wyss-Coray have developed VINE-seq to address this.
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