One way to think about it is to include what is absolutely necessary ( omitting the section will break the paper) or what is supporting evidence. Keep in mind that in a paper you are telling an interesting story, not telling the reader every single experiment you have done. For example, some supporting control experiments can be moved to the supplemental data. Just mention the results in the main text, and refer to the supp file for details. Another option is try online journals such as Plos/BMC series, which allow for much longer manuscript.