Runx1 marks a luminal castration resistant lineage established at the onset of prostate development

We performed scRNA-seq to characterize the heterogeneity of RUNX1+ and RUNX1- fractions of the adult mouse prostate. We dissected individual lobes of intact/hormone naive and regressed/castrated mouse prostates, isolated from P2-Runx1:RFP reporter mice, expressing RFP as a surrogate of Runx1 expression. In order to compensate for the relative sparsity of RFP+ and RFP- cells respectively pre- and post-castration, we artificially enriched for under-represented populations by FACS (EPCAM+) prior cell encapsulation. To study the specification of embryonic prostate lineages, we performed scRNA-seq on the EPCAM+ fraction of UGS explant cultures collected at successive time points: E15.5 (D0), day 1 (D1), day 3 (D3), and day 6 (D6). For adult mouse prostate samples, intact and castrated lobes were dissected from P2-Runx1:RFP mouse models. Individually sorted populations (ECPAM+ RFP+ / RFP-) from each lobe were multiplexed using MULTI-seq lipid-tagged indices. 3 independent experiments (run 1, run 2, run 3) were performed. For UGS explant cultures, samples were collected at successive time points of cultures: E15.5 (D0), day 1 (D1), day 3 (D3), and day 6 (D6). Sorted populations (EPCAM+) were multiplexed using MULTI-seq lipid-tagged indices.