Experimental Details to Report in Your Manuscript

Experimental Details to Report in Your Manuscript


Publication of research articles is based on the principle that results must be independently verifiable. Therefore, authors are expected to 1) describe the experiments performed and present the results as accurately as possible, 2) make unique reagents and resources available to qualified investigators either directly or through a recognized distributor and 3) store all data that are reported in the manuscript either on a secured server at their research institution or in a public repository. For more information on APS’s efforts to enhance experimental reproducibility, see Promoting Transparent Reporting in APS Publications to Enhance Data Reproducibility.

Descriptions of the following materials are encouraged to include:


Cell Lines

  • Source of cells utilized (species, sex, strain, race, age of donor, whether primary or established)
  • Declaration of whether cell line authentication was performed and by what method (e.g., STR profiling)
  • Declaration of whether testing for mycoplasma contamination was performed and the results of the tests

Reagents and Unique Materials

  • Source of reagents and unique materials (Company name, distributer, developer, etc.)
  • Data that confirms the specificity of the unique biological, biochemical, and/or immunological markers, submitted as “Supporting Data.”  If the data already exists, please reference the published article.

Antibodies

  • Source of antibodies (company name, distributer, developer, etc.)
  • magnifying glass One representative full blot detailing the validation of the each antibody used in the study for protein specificity, excluding loading controls.
    • Lanes on the blot should be labeled to note the nonspecific and specific bands  and the positive and negative controls. Exposure time should be indicated.
    • Validation data should be submitted as Supporting Material for Reviewers Only.  If the data already exists, please reference the published article.  

Description of the following studies should include:


Animal Studies

  • An explicit statement that the animal use protocol was submitted to, and approved by an institutional committee or that the protocol was performed under a license obtained from such a committee, board, or governing office
  • magnifying glass Authors are encouraged to refer to the ARRIVE Guidelines Checklist in preparation for reporting the methods and results of animal studies.  Particular attention should be given to providing detailed information regarding:
    • Precise details of all experimental procedures (drug formulation and dose, anesthesia and analgesia used, method of euthanasia, etc.)
    • Steps taken to minimize subjective bias in the study design (randomization, blinding, etc.)
    • The animals used in the study (species, strain, sex, age, source of animals, genetic modification status, housing, diet, etc.)
    • The controls used in the study (littermate, purchased, identical conditions, contemporaneous, historical, etc.)

Human Studies

  • An explicit statement that the protocol was submitted to, and approved by, an institutional review board or the protocol was performed under a license obtained from such a committee, board, or governing office
  • The sex and/or gender of participants
  • If the study is a clinical trial, a statement of registration is required

Information for the following data and analyses should include:


Electrophoretic gels, blots, and other digital images

  • Each gel or blot should contain a molecular-weight size marker
  • Each panel should retain space above and below the band of interest from the original image
  • All micrographs should include a scale bar
  • Images presented in the manuscript should faithfully represent those originally-captured:
    • Authors should not move, remove, introduce, obscure or enhance any specific feature within an image.
    • Authors should not adjust contrast, color balance or brightness unless applied to the entire figure. However, these adjustments must not obscure, eliminate or misrepresent the originally captured information. Any non-linear adjustment should be disclosed in the legend.
    • Authors should not quantitatively compare samples from different gels/blots; if this is unavoidable authors must state in the legend that all samples were derived at the same time and processed in parallel.
  • If gels, blots, or fields are grouped or rearranged, then authors must insert spaces or dividing lines to indicate these changes and disclose the arrangement in the figure legend.

Mathematical Models

Presentation of the model(s) must be sufficiently clear to allow physiologists with limited experience in modeling to follow the model development, limitations, and physiological relevance. Assumptions concerning the importance of physiological processes included in the model should be clearly stated.

  • If the model equation(s) require solution, the method of solution should be described in sufficient detail to permit readers to duplicate the solution in their own laboratories. Algorithms from commercial software libraries should be so identified. Details of the solution strategy may be summarized in an Appendix.
  • For simulations, sources or estimation methods for all parameter values should be presented and the numerical values given in the text or a table. A sensitivity analysis must be performed for important parameters (covering ranges of values relevant to the manuscript) to determine how the model predictions are affected by numerical parameter values.
  • If the model is used to estimate parameter values, measures of the uncertainties associated with the estimated parameter values should be presented.
  • For models intended for use in a predictive setting, validation of the model with a data set not used for model parameter estimation (i.e., cross-validation) is recommended. Sensitivity analysis or parameter uncertainty determination is an important component of modern modeling practice that allows assessment of the validity of a model.
  • Results obtained with the model(s) should be compared with appropriate physiological data, either from literature or from new experiments. Simulation results may be examined for prediction of changes or trends in physiological variables similar to those reported for in vitro or in vivo studies. The discussion should include information on the physiological significance of the model study, limitations of the model, and suggestions for new modeling and/or experimental studies.

Statistical Analyses

Provide the experimental data and results as well as the particular statistical significance of the data.

APS has published an editorial on the use of statistics, and authors are encouraged to consult it.


Data Repositories

Data reported in the manuscript should be stored in appropriate repositories such as those found at the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI).and the repository used should be reported in the Methods Section. Data that should be deposited include:

  • Nucleic acid/amino acid sequences (Genbank)
  • Sequence data (UniProt)
  • Other special types of data (e.g., genomes, bulk submissions) may be submitted to:
    • DDBJ - DNA Data Bank of Japan
    • EMBL - EMBL Nucleotide Sequence Database
    • GenBank - National Center for Biotechnology Information
  • Microarray data, complete data set, should be submitted  to one of these two databases prior to manuscripts submission: the NCBI Gene Expression Omnibus (GEO); or the EMBL-EBI ArrayExpress repository. Information for accessing the microarray data should be included in the article’s Materials and Methods 
  • Genome-wide datasets using next generation sequencing (e.g. massively parallel sequencing) should be submitted to a compatible database such as the Gene Expression Omnibus (GEO) using the instructions and data formats supported by the database. Examples of this include RNA-Seq, ChIP-Seq or sequence modalities designed to examine epigenetic regulation. Authors should provide the set of login credentials (username and password) that will allow referees access the data set during review, if it is set up as a private resource.

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