Common Sins When Publishing Your Paper
When it comes to publishing your paper you want to show the world what excellent research you’ve worked so hard to produce. Part of that is providing enough detail so that others can reproduce your work and take it further. There are certain details you need to include in your paper; many, but not all journals require these details. But even if the journal you are submitting to does not ask for these you should always include them. So what details am I talking about? Well in order to point out the crucial details I’m going to point out some of the common sins people make when publishing their paper:
Methods are obviously a crucial part of your research and all journals will require a Methods section in your paper. But the level of detail required will vary. One of the common sins that you’ll see is people referring back to previous papers for more detailed methods.
This may save you time and space in your write-up but if you’re not careful you’ll risk sending people on a wild goose chase going from paper to paper all of which cite ANOTHER previous paper for more detail. So include all the detail in your current paper that someone will need to perform the experiment.
There are standard protocols that you won’t need to share with your readers, for example, there is no need to write a step-by-step guide on how to run an SDS-PAGE gel. But some details are experiment specific. Make sure you include details such as the media you grew your cells in if it isn’t the standard for that cell line, or amounts of recombinant protein you used in your assay.
Including these details is not only important for your readers but you might find it useful yourself if you need to go back and perform an experiment from a paper you published a while back. There are also some guidelines for specific experiments or fields for what needs to be reported, such as the MIQE guidelines. These provide standards for reporting quantitative realtime PCR experiments.
Lack of reagent details
One of my pet peeves is people not including company and catalogue numbers for reagents. I’ve seen papers saying they performed a western blot using an antibody for protein X but no sign of where the antibody was purchased, and given the number of antibody companies out there, it is impossible for someone to figure out just which one you used.
While including the company name is a step forward, it still isn’t enough. Quite often companies will produce more than one antibody against the same protein, so including the catalogue number will ensure that people can use the same reagents you did. This also applies to reagents that you have designed yourself, such as vectors, mutant proteins and primers.
If you can’t include details such as vector maps or primer sequences in the main paper due to space restrictions, include them in the supplementary materials. Many journals do not have a limit on the size of supporting information and will be happy you included these details.
Not making reagents available
Did you create a new vector? Perhaps you even generated your own antibodies, for example phosphorylation site specific antibodies. Or you might have created stable cell lines expressing your protein. You should, wherever possible, make these reagents available to the community. There are various ways, but the most common are to include a corresponding author e-mail address and to deposit your reagents in a repository. Including a contact e-mail is great, but ensure this e-mail is one that will be accessible to the lab for the long term, don’t use your PhD students address if they are leaving the lab shortly as this will likely be shut down or inaccessible.
The slightly more time consuming (at least initially) process is to submit your reagents to a suitable repository. This may seem like a lot of work to begin with, but once they are deposited you don’t have to worry about responding to requests or ensuring you don’t sent off the last remaining stock you have. There are many different repositories available out there including Addgene (for plasmids) and The ATCC Biomaterial Contributor Network (for cell lines and microbial strains). Main institutions may also have their own repositories and will handle MTAs (material transfer agreements) for you. If you do deposit your reagents in a repository, ensure you include these details in the paper so people know where to access them.
Not making raw data available
With many experiments nowadays producing massive amounts of data (think genome sequences, microarrays, RNA-seq and mass spectrometry) it is important that this raw information is accessible. It is impossible to include all of this data in a paper, although some of it may be suitably incorporated into the supplementary materials. Therefore ensure your raw data is available by depositing it into a repository.
There is a wealth of repositories available for such ‘big data’ including European Nucleotide Archive and GenBank for sequencing data, assemblies and annotations, miRBase take submissions of published miRNA sequences, while Figshare takes a variety of submission types from images to videos. If you are dealing with sensitive data, such a patient data ensure that you are submitting your data to a suitable repository. Such sensitive data needs to be handled in an appropriate way in order to conform to ethics.
Know of any other publication sins? Leave us a comment below!
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