Protocols Instructions

A. Protocols must be validated by at least one of two methods: 1) having been used in at least one published primary research paper from the lab of the authors of the submission (a representative dataset should be added whenever possible) or 2) data must be provided demonstrating the protocol’s validity to be assessed during the review process (this should be included in the Supplemental Data).

B. Submissions must represent a significant expansion of the information available in the supporting paper(s) and must be appropriate to the scope of SLAS Discovery. Purely computational protocols will rarely be appropriate.

C. Authors must upload, along with their manuscript, at least one of the following:

i. At least one supporting primary paper from the author’s lab where the method has been used.

ii. Any other publication(s) focused on the method with one or more authors in common with the submitted protocol.

iii. Representative Supplemental data if i and ii above are not available.

D. Protocols using live vertebrates, higher invertebrates or human subjects are expected to conform to relevant guidelines and regulations and this should be stated in the manuscript.

A template has been created to assist you in preparing your Protocol submission. It can be downloaded here.

Submissions should consist of at least the following 4 sections.

The introduction should include:

1. A description of the development of the protocol. Publications using the protocol as described in section 1.C should be cited here.

2. Comparison with other methods, and a discussion of the advantages and disadvantages of the protocol compared to alternatives if such alternatives exist.

3. A discussion of requisite controls.

4. A description of any specialized expertise needed to implement the protocol.

5. A discussion of any limitations of the protocol or of conditions that would be expected to cause it to fail or yield unreliable results.

A list of all essential materials should be provided, with reagents and equipment listed in separate sections.

a. Reagents: if it is known that any reagents must have certain characteristics or be obtained from specific sources for the protocol to succeed, this should be indicated and detailed ordering information should be included. Details should be provided regarding key steps in preparing critical reagents. If samples must have certain specifications for the protocol to work, this should be stated. The composition of any unique buffer should be provided in full using a tabular form. Items that must be made up fresh should be identified as such, and storage conditions and stability for those that do not need to be prepared fresh should be defined.

b. Equipment: In cases where only a specific piece of equipment or instrument is suitable, this should be stated clearly and the model and manufacturer should be noted. Otherwise, the general capabilities of equipment and instruments required should be listed.

c. Software: Key software needed for conducting or analyzing the experiment should be identified. If software is publicly or commercially available, the version and operating system should be specified, and any extensions, image acquisition settings or macros needed must be listed and sources should be identified. If custom software is used, code should be deposited on a public repository and detailed instructions must be provided that will allow a user to download and run the software appropriately.

1. A numbered list of direct experimental instructions should be provided. If the protocol involves distinct stages (i.e. sample preparation, instrument setup, measurement) include these in the list as separate headings. The approximate length of time each stage and each step in a stage takes should be indicated, as should the time needed to complete the entire protocol. If there are points at which the protocol can be paused, these should be indicated any storage conditions needed for successful resumption of the protocol should be noted.

2. Steps involving the mixing of several components should be provided in a tabular form for clarity. Always specify quantities and concentrations in SI units.

3. Specify any critical steps that must be followed exactly for the protocol to succeed. Centrifugation speeds should be given in g, or, if using rpm, the model of centrifuge and rotor should be specified. Centrifuge time and temperature should be specified.

4. A troubleshooting subsection should be included in which potential problems should be discussed explicitly. Key indicators that a problem has occurred should be described along with the appropriate corrective action. It may be most effective to include this in the form of a table. The step in which the problem occurs should be noted.

5. A flow diagram of the entire procedure should be provided, with break points, critical steps and potential problems indicated.

6. Specific instructions for data analysis must be included that are sufficiently detailed to allow a user to replicate all procedures. Sample data should be provided allowing readers to replicate the analysis on their own system. Examples of items that should be specified include (but are not limited to): details of masking, background subtraction and object selection for high-content imaging, gating for flow cytometry, and densitometry and background subtraction for immunoblotting. Equations needed to fit data curves, calculate results and procedures to interpret them should be provided.

1. Information about the likely outcome of protocol should be provided. Criteria that can be used to determine the protocol’s success should be defined. If there are points at which specific criteria must be met before proceeding to the next step, these should be noted and should be included in the flow diagram.

2. It is desirable to include one set of data from an experiment that worked well to help guide readers.

1. Citations of one or more papers where the method has been used

2. Background info if citations included in the Introduction