RNAseq anaysis of entorhinal cortex layer II neurons upon Ptbp1 modulation

Purpose: To identify gene expression changes in entorhinal cortex layer II (ECII) neurons upon Ptbp1 modulation (silencing and overexpression) Method: bacterial artificial chromosome - Translating Ribosome Affinity Purification (bacTRAP) to isolate actively translated mRNA in ECII neurons, 2 weeks after stereotaxic injection of an AAV1 vector in the EC of ECII-bacTRAP mice; followed by RNAseq. Note: Ptbp1 was significantly overexpressed in the overexpression experiment, but no silencing was achieved with the silencing vector, probably because of tight control of Ptbp1 expression Overall design: in IP162 (silencing), 5 mice injected with a scrambled-mcherry vector, 5 with a Ptbp1 shRNA-mcherry vector; 1 Ptbp1 shRNA mouse was excluded because no read mapped to mcherry; in IP170 (overexpression), 5 mice injected with control-mcherry vector, 5 mice with a Ptbp1-mcherry vector; 1 control mouse was excluded because no read mapped to mcherry; in both experiments, the two entorhinal cortices were pooled