It is usually most efficient to write this section once the results are completed. Take your protocols and lab journal and gather all documents you used to perform the experiments shown in the manuscript figures. However, describing the materials and methods does not require all that much creativity or elegant writing skills, so drafting this section first is a good way of getting into the writing process. A somewhat scary empty page is quickly filled simply by placing information from your lab journal there.
Use past tense in the material and methods section, as you already performed the described experimental methods in the past.
The standard sentence defining this section is: It should describe the applied material and methods in such a detail, that other scientists are able to replicate the experiments.
Structure this section in a logical order; this might be the same order as shown in the results section, but does not have to. At the beginning you should describe your test system (animal, cell system). When working with animals the ARRIVE guidelines provide a good overview, which information you should provide about your animals. Depending on performed experiments, it can be useful to provide very detailed information, for example, including the breeding scheme or very detailed housing conditions as this may influence results like behavioral tests or breeding success.
Work with Antibodies
When you worked with antibodies, you should list all details about primary and secondary antibodies, like antigen, host, order ID. It is also useful and sometimes asked for by the journal to add the unique antibody ID provided by the antibody registry. When using several antibodies, a table listing all information can help to provide information well-structured. Tables also help to structure listings of other often used materials like patient information, oligomers for PCR, viruses and many more.
When you used a commercially available kit for any kind of analysis and used the protocol provided in the kit, you can state it. To make it easier for the reader, you should still provide a very short description of the method. The same applies, if you used a method that was previously already described in another article. You can state “as previously described by…” but should still shortly describe the method. Very important is also, that you cite the primary article and not an article that also states “as previously described by…” as this can end up to be a long search for the reader if she/he wants to find the original article.
Focus on Relevant Experiments
Usually, you should describe only the experiments that are directly relevant to the results in the manuscript. Mentioning additional materials and methods (for example analysis of animal organs that are off topic for your study) confuses the reader and may lead to questioning your results. However, additional experiments may still be relevant to your study if they could change the results shown in your manuscript. A typical example are behavioral tests that were performed prior to the ones shown in your manuscript, because animals may not be naïve to the test environment, or be stressed or tired from previous tests. Often the results of such additional experiments are mentioned in the text with the remark “data not shown”. Alternatively, they could be included as supplementary material, which is an option provided by many journals.
By now, many journals ask you to provide all raw data of your study so readers are able to re-evaluate all performed analyses. There are different options to provide data. You can store data in an online depository, that is provided by the journal or an independent provider or you can provide data in a supplementary file that is submitted with your manuscript. The latter option is only feasible if raw data are not too large. Additionally, many journals also suggest to store protocols used for the manuscript in an online depository for protocols. The Authors Guide will provide you detailed information about available options for raw data and protocol depositories.
Today’s conclusion about the Material and Methods section:
I:
Write this section in such a detail, that the reader is able to replicate your experiments
