Our paper which describes the components of the placenta transcriptome which are conserved among all placental mammals in Placenta just came out today. More importantly than the results and the text of the paper, though, is the fact that all of the code and results of this paper, from the very first work I did two years ago to its publication today is present in git, and (in theory) reproducible.
You can see where our paper was rejected from Genome Biology and Genes and development and radically refocused before submission to Placenta. But more importantly, you can know where every single result which is mentioned in the paper came from, the precise code to generate it, and how we came to the final paper which was published. [And you've also got all of the hooks to branch off from our analysis to do your own analysis based on our data!]
This is what open, reproducible science should look like.