Picture this: You’re a new postdoc, starting a research project in your lab. You’re so excited to have a new project all your own — you’re full of hope and ready to get started. Your project builds off of someone else’s research, and the first thing you need to do is replicate their results so you can start learning new things about your model system. Easy, right?
Wrong. You take a look at their methods section only to find that the details are seriously lacking. You know what cells they used, but where did they get them? You have the names of their antibodies, but which ones did they use? At each step, you’re stuck troubleshooting, titrating, and spending lots of valuable time trying to recreate previous results. Not exactly the start to your new research project you had hoped for.
This scenario happens in labs around the world every day — reproducibility is a major crisis in research. The scientific community is beginning to establish universal standards for methods reporting, and community efforts such as the Materials Design Analysis Reporting (MDAR) checklist and the EQUATOR network are leading the way. Reporting standards have become increasingly important to scientists for several reasons:
- Wasted efforts to replicate data with insufficient methodological information is time-consuming, expensive, tiresome, and wasteful — and it leads to public mistrust of science.
- In order for any experiment to be done well, a researcher must be able to build off of other research, which is impossible if key details are not provided.
- Basing future research — or even health policy decisions — on shaky, irreproducible research can have major health impacts.
- Due to these concerns, research funders and journals are developing policies that require compliance with basic reporting standards for researchers associated with their organization.
Fortunately, these issues can be addressed by including the right information in your manuscript. In addition to helping others reproduce your results, adding sufficient methodological details also helps readers understand the conditions in which your results are applicable. This saves others from spending tons of time and effort on reproducing results and helps move science forward more quickly.
In this article, we’ll talk about what you need to add to your Materials and Methods section to help others reproduce your study.
Cell lines are a model organism
It’s important to note that eukaryotic cell lines are meant as a type of model organism; that is, when used properly, they should yield reproducible results through repeated experiments. This helps others to build off of your results — but in order for that to happen, important details must be included in your methods. First, the source of your cell lines must be clearly indicated. If that source is commercial or you got your cell lines from the ATCC it is helpful to include the manufacturer’s catalog number (e.g., C505003 for TOP10 cells from ThermoFisher) or the Research Resource Identifier — that way, other researchers can obtain the same cells you did. If your cells were borrowed from another lab, you should list the primary investigator’s name, and if you generated your own cell lines, the methods should be clearly described in your manuscript.
In addition to the source of your cells, you should also describe whether - and how - you authenticated your cells. Cell line contamination is common and can drastically affect results, so authenticating your cells periodically can help to ensure that your cells are what you think they are. In addition to authentication, cell lines should also be tested periodically for mycoplasma, and you should include the results of that testing in your methods section.
...and so are research animals
Whether you use mice, sheep, monkeys, or fruit flies, your research animals should be considered critically important to the reproducibility of your study. In order for your research to be interpreted - and repeated - you need to thoroughly describe the animals you use. In addition to the species and strain (e.g., C57Bl/6 mice), you should also describe the source (with identifiers if you obtained your animals commercially) and the age and sex of the animals used. If your animals were housed in your research facility, it helps to describe the location, equipment, food, light/dark cycle, and other information about how the animals were housed. If your animals were obtained from the wild at any point, you should describe how they were captured and transported. For all animals, the end-of-experiment protocol should be described (e.g., were the animals sacrificed, kept for other experiments, or released?)
Similar considerations apply to plants and field samples
Similar to research animals, plants and samples obtained from the field (e.g., water from a pond or rice from a paddy) must also be described clearly. The species and strain should be described where appropriate, along with the source - with either enough information to obtain them commercially or a clear description of where the samples were obtained. For samples obtained from the field, permissions should also be described. Again, housing parameters and storage should be described as thoroughly as possible because they can affect the results of the study.
Provide enough information about your equipment and reagents
When you repeat an experiment from someone else’s study, the most frustrating part can often be finding enough information about their reagents and equipment. These details are often left out of methods sections, but they’re critical to understanding exactly what was done. When you describe your experiments in your methods, make sure to include the manufacturer and model number of equipment such as flow cytometers, thermal cyclers for PCR, and spectrophotometers. For all reagents used - even cell culture media, PBS, and gels for electrophoresis - you should indicate the source and catalog number, or a brief recipe for lab-made reagents.
And then there are antibodies
For antibodies, a few more details are needed. In addition to source and catalog number, the clone number and lot number should be provided. The dilution of the antibodies should be described in your methods, too - even if another researcher needs to titrate, this gives them an idea of where to start and helps to explain variations in results. It helps to describe the validation of your antibodies, too. If they were validated by the manufacturer for your specific system, you can simply include a reference to their website, but if you use your antibodies in a different system, you should describe how you made sure that the antibodies worked in your system. For example, did you use an isotype control to confirm the specificity of the antibody in your cells? A brief description of your methods can show readers that your results are trustworthy.
Keep a checklist
Once you’ve written your Methods section for your manuscript, it can help to go through a checklist. Here’s an example based on the information we’ve covered above:
- Cell lines: source, catalog number, authentication, and the results of mycoplasma testing
- Animals: species, strain, age, sex, housing, source, and end-of-experiment protocol
- Plants: source, species and strain, housing parameters and storage
- Equipment and reagents: Manufacturer, model number, source, catalog number
- Antibodies: catalog number, source, clone number, lot number, dilution for each type of experiment
A little detail goes a long way
Including all of these details may seem like a pain - do you really need to dig through the freezer to find the lot number of your antibody? Will anyone really care which thermal cycler you used for your RT-PCR? However, this information is critical for anyone looking at your research. Ideally, you’d have included it in your lab notebook from the beginning, but if you haven’t, you’ll need to take the time to dig up those details to make your manuscript complete.
Let’s go back to the scenario we described at the beginning: you’re just starting out in a new postdoc position, and you’re so excited about your new project. You go to the literature to get started on your project — and you find all the details you need. You order the reagents and cell lines, get your antibodies ready, and start by following their methods to replicate a previous finding. You see what the other researchers saw, and you’re able to use that information to start asking new questions. These early experiments are the foundation for your new research project — and your career. Isn’t that a better start?
Do you want to be sure that your manuscript meets the highest standards for reporting? Research Square offers a Methods Reporting Badge that evaluates methods-related reporting and more. Learn more here!