The entire set of experiments you have performed to set up your controls and basics of your projects may not be necessarily what your readers want to know. The order of your experiments is another matter. Your paper does not have to follow the same order as you did in your project. You may need to shuffle the experiments in order to come up with a compelling and logical story that is worth publishing in a peer reviewed journal.
Find the hot findings of your study. Discuss them with experience scientists, colleagues, and friends. try to wrap up a story that make sense rather than indicating how hard you have worked and how many exciting experiments you have done to come up with this conclusion. Put yourself in the readers shoes.