In vivo 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, 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 10X 3' scRNA-seq. All 5 mice listed here are biological replicates, done across 3 batches (B1_1, B1_2, B2_1, B2_2, B3_1). The 18 genes are:  mSafe1, Trem2, Rraga, Flcn, Fasn, Olig2, Gfap, Clu, Dpp6, Tbk1, C9orf72, Cfap410, Stk39, Lrrk2, Ndufaf2, Sh3gl2, Srf, Rbfox3.