The median gene count per cell was much lower than the total gene count. This means that there must have been a lot of different gene combinations within the cells to account for the fact that the total gene count is much higher. So even without doing a thorough analysis, we can say that our data captured the heterogeneity from the hypothalamus very nicely.
The plots on the top genes and spliced reads show that there were some issues with ambient RNA. The mitochondrial genes were very dominant, and the high percentage of spliced reads shows that there were a high number of reads coming from the cytoplasm instead of the nucleus. This issue can be solved later in the analysis, when a better cell selection can take place, by aggregating multiple samples.
Even though the plots on enrichment around the transcription start site looked like they are supposed to look, the clustering plots clearly showed that one of the samples was compromised. Several steps of the lab protocol will have to be repeated for that specific sample.