Data that are integral to the manuscript but impractical to include in the printed journal (for instance, large-scale data sets and videos) may be presented as Supplementary Data. Data and information that are peripheral to the conclusions may be provided as supplementary data if the editor agrees that these data would be valuable to specialist readers and are not necessary for other readers to understand the experimental support for important claims and conclusions; all data that are directly relevant to, and necessary for support of the central claims and conclusions of the article must be presented in the manuscript itself. Authors should note that the function of supplementary data is to provide an opportunity to present data and information that would not normally be published in the print journal, rather than to reduce article length. Important control experiments should always be presented in the manuscript, whereas assays that merely demonstrate that a reagent is suitable for use in an experiment (for instance) may be presented as supplementary material with the permission of the coeditor. Detailed experimental protocols that would be of interest only to specialists and are not necessary to support the central claims and conclusions are also permissible in Supplementary Data. Use of phrases such as "data not shown" or "unpublished results" is discouraged in the print article; instead, authors are encouraged to present such data as supplementary material.
Large-scale data sets. Large-scale data sets (e.g., complete or draft genome sequences, genome annotations, genetic maps, EST data sets, transcript profiles, proteomic data sets, and metabolic profiles) that are integral to the manuscript must be provided at time of manuscript submission. At time of submission, large-scale supplementary data must be placed in a permanent public repository (e.g., GEO http://www.ncbi.nlm.nih.gov/geo or Array-Express http://www.ebi.ac.uk/arrayexpress), as it will not be stored at Molecular Plant Online site permanently, only during the review process. Non-permanent URLs should also be provided if authors want to make available imaging or other software with unusual file types requiring special software downloads or those that are not compatible with Molecular Plant Online site. In general, large-scale data sets must be complete (e.g., must include the complete set of genome sequences analyzed, ESTs identified, genes queried in transcript profiling, peptides identified, molecules identified, etc.) and should be provided in Microsoft Excel format.
Data supporting transcript profiling experiments must include complete sequence information (e.g., accession numbers, any relevant annotation data, and in the case of Arabidopsis, TAIR locus identifiers [http://www.arabidopsis.org]). Authors are encouraged to follow the MIAME (Minimal Information for a Microarray Experiment) standards. See Methods for expectations of experimental design, analysis, and reporting.
All supplementary materials will be reviewed as part of the normal manuscript review process. Supplementary materials must be briefly described in the manuscript (in the Results or Methods section, as appropriate) with direct reference to each item, such as "Supplementary Figure 1 online," "Supplementary Table 1 online," "Supplementary Protocol 1 online," "Supplementary Movie 1 online," etc. (numbering should always start at 1, since these elements will be numbered independently from those that will appear in the printed version of the article). A brief descriptive title of each piece that is to be posted online should be listed at the end of the Methods section under the heading "Supplementary Data". All legends to movies should be together in a separate word processing file (such as Microsoft Word), entitled "Legends to Movies." Legends to supplementary figures should be placed below each figure, not in a separate document, and should follow the same guidelines as for article figure legends (see above). Supplementary tables should include any relevant footnotes.Methods for experiments presented as supplementary material must be described in the print article, at least in general terms; a more detailed methods description may be provided as a Supplementary Protocol. Any references associated with Supplementary materials should be placed with the relevant text, table, or figure.
A complete list of supplementary references, with the title "Supplementary References," should also be placed in the manuscript following the regular references. Text such as in legends, footnotes, and protocols must follow journal style. Supplementary materials are subject to the same copyright restrictions as published manuscripts and cannot be presented elsewhere without proper citation.
At the time of submission, the manuscript, figures, and easily converted supplementary data (figures, small tables, and text) will be converted together into a PDF for review. Movies, movie legends, and large datasets will be uploaded separately as "Additional Supplementary Files." Preferred file formats for uploading are Microsoft Excel (.xls) for large-scale data sets, PDF or .jpg for figures, QuickTime (.mov), .mpeg, or .avi for movies, and PDF for text and tables. File sizes should be no larger than 10 MB.
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