In vivo Spatial Perturb-Seq in the mouse brain
Functional genomics that knocks out individual genes is ideal for investigating gene functions. Examining these perturbations in vivo, within native tissue architecture and with spatial context, is crucial for accurately assessing the impact of genetic modifications both within the cell and on its microenvironment. Overall design: We stereotaxically injected an AAV library targeting 18 genes directly into the mouse hippocampus to induce sparse perturbations, then performed Stereo-seq. The 18 loci that are targeted are: mSafe1, Trem2, Rraga, Flcn, Fasn, Olig2, Gfap, Clu, Dpp6, Tbk1, C9orf72, Cfap410, Stk39, Lrrk2, Ndufaf2, Sh3gl2, Srf, Rbfox3. The dataset here consists of 2 coronal hemisphere sections from 1 mouse.