I am currently in the process of additional experimentation to try and convince the reviewers (sound familiar?) to add into supplementary material. However, some of the methods I am using to produce this data are not used to produce any of the figures in the main manuscript. So I'm not completely sure where to mention these methods. Would it be in the main materials and methods section of the manuscript making reference to the supplementary figure? Or would I briefly describe the method in the supplementary figure legend? Any help would be greatly appreciated as this is my first time going through the publication process firsthand. The journal is Infection and Immunity if thismakes a difference.
If the journal has not mentioned a number-of-words-limitation for the type of the paper you have submitted, then you can add the extra methods inside the paper. Otherwise, you may add in appendix and reply to the reviewers that because of the journal's requirements and limitations in number of words, we added the related methods to Appendix or Supplementary file.
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