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Supplemental Material & Data

Supplemental Material Submission Instructions

Deposit of Primary Data

Supplemental Material Submission Instructions

What to Submit as Supplemental Material

Supporting material that cannot be included, and which is not essential for inclusion, in the full text of the manuscript, but would nevertheless benefit the reader. It should not be essential to understanding the conclusions of the paper, but should contain data that are additional or complementary and directly relevant to the article content. Authors are encouraged to take advantage of the opportunity to submit Supplementary data whenever appropriate; for example, when the amount of material is too great to warrant inclusion in the main body of the paper, or when the material is in a format that cannot be represented in print (i.e. video clips or animated graphics). Please note that atomic co-ordinates used to create molecular models described in a manuscript, unless deposited in a publicly available database, must be made available as Supplementary data.

All material to be considered as Supplementary data must be submitted at the same time as the main manuscript for peer review. Please indicate clearly the material intended as Supplementary data upon submission. Also ensure that the Supplementary data is referred to in the main manuscript at an appropriate point in the text. It cannot be altered or replaced after the paper has been accepted for publication. [Supporting material that has not been peer reviewed will not be published as Supplementary data (so will not be designated 'S' in the Table of Contents), but can be made available through a link to the author's home page, at the discretion of the Executive Editor handling the paper. The word 'Supplementary' must not be used to describe this material. Please use words such as 'Supporting material' or 'Additional material'.

Supplementary data should be submitted in a separate file(s), in its final form. Please note that Supplementary data will not be edited, so ensure that it is clearly and succinctly presented, and that the style of terms conforms to the rest of the paper. Also ensure that the presentation will work on any internet browser.

Note: Supplementary data is considered as published material and is regulated by the same copyright and permissions rules as the published article to which it belongs.

Metadata

Although we do not limit the number or type of Supplemental Material items authors may include, we do require that they provide a relevant and useful expansion of the article, and that they be as well described as are figures and tables included within the body of the article. Good metadata of this material are key to discoverability and usefulness. All Supplemental Material should include the following:

  • Type and number: Supplemental material can be named in almost any way, provided that the files are consistently named, and numbers are preceded by “S” and closed with a period. Examples:
    • Figure S1.
    • Table S1.
    • Text S1.
    • Video S1.
    • Animation S1.
    • Alternative Language Abstract S1.
  • Figures, Tables, Videos, Animations should be provided with titles should be no more than 15 words and set in bold type, using sentence case.
  • Supplemental material figures and tables should follow the requirements for main-text figures and tables (seeFigure PreparationandTable Preparation).
  • Other types of supplementary material files should include a caption of no more than 300 words should, describing the key message of the figure/video/animation in such a way that readers can interpret the file without referring to the text.
  • Citation In-Text

    All Supplementary data MUST be referred to in the main manuscript at an appropriate point in the text, just as main text figures and tables. This offers readers context and allows for seamless interlinking. Text citations should use the appropriate type and number designation (e.g., Video S1). Supplementary data should be made available by the publisher as online-only content, linked to the online manuscript. Such data should consist of electronic files and should not merely be a link to another web site.

    Acceptable formats

    The supplementary data should preferably be saved as one single PDF file, including all text, figures, tables and legends. If this is not possible, a maximum of 10 files is acceptable to make up the supplementary data unit for the article.We prefer that Supplemental Material files not exceed 10MB. However, if that size limit results in a loss of quality (e.g., by making the dimensions smaller or compressing a movie in such a way as to compromise image quality), we can accept larger files.

    Text files

    Supplementary text should be submitted as text files in MS Word (.doc), HTML (.php) or RTF (.rtf) format.And should be mentioned appropriately in text.

    Spreadsheet files in MS Excel (.xls) or CSV format. Where possible, combine all tables into a single Excel workbook, saving individual tables on separate clearly labelled worksheets (tabs).

    Figures

    Supplemental figures should be submitted as separate tif, gif or jpg files at a minimum resolution of 300 ppi, just as with main figures (please see ourFigure Preparationsection for detailed instructions on figure preparation).

    Videos & audio clips

    For videos, please try to submit videos &audio clips of reasonable quality. We highly recommend videos to be submitted in MP4 formatand audio clips in mp3 format.Whatever format you use, videos must open and play in either QuickTime Player v. 7.6.2 or Windows Media Player v. 11.

    Authors who have video and/or audio clips that they wish to submit their article are strongly encouraged to include these within the body of the article. This can be done in the same way as a figure or table by referring to the multimedia content and noting in the body text where it should be placed with its associated caption.

    Help

    If you require further help or information regarding submission or preparation of Supplementary data, please

Deposit of Primary Data

An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims. Therefore, a condition of publication in a TXT journal is that authors are required to make materials, data and associated protocols promptly available to readers without undue qualifications. Any restrictions on the availability of materials or information must be disclosed to the editors at the time of submission. Any restrictions must also be disclosed in the submitted manuscript, including details of how readers can obtain materials and information. If materials are to be distributed by a for-profit company, this must be stated in the paper.

Data sets will be made freely available to readers from the date of publication, and must be provided to editors and peer-reviewers at submission, for the purposes of evaluating the manuscript.

For the following types of data set, submission to a community-endorsed, public repository is mandatory. Accession numbers must be provided in the paper. Examples of appropriate public repositories are listed below.

Deposition of sequence and structural data

Sequence information, co-ordinates used to create molecular models described in a manuscript, and structural data must be submitted in electronic form, prior to acceptance, to the appropriate database for release no later than the date of publication of the corresponding article in the Journal. Deposition numbers and/or accession numbers provided by the database should be included in the manuscript and entered into the relevant boxes during online submission or communicated to the Executive Editor handling the manuscript as soon as received. In cases where there may be no appropriate database, authors must make their data available on request. Atomic co-ordinates may be included in the publication as supplementary material. Manuscripts will not be published until the Journal is in receipt of the deposition number.

For papers reporting novel nucleic acid sequences

Nucleic acid sequence information must be deposited with one of the three major collaborative databases (EMBL/GenBank/DDBJ). For sequences obtained from a public or private web site, it is the author's responsibility to ensure that any sequence used within the manuscript is deposited before publication. It is necessary to submit sequences to one database only since data are exchanged between EMBL, GenBank and DDBJ on a daily basis. New sequence names and their accession numbers should be listed at the beginning of the Materials and Methods section to aid searches by readers. In order to allow new methods of data search,NAR encourages authors to cite GenBank accession numbers when referring to established sequences within their manuscript.

For Illumina-type sequencing, authors are encouraged to submit raw Illumina data to the NCBI’s Sequence Read Archive, and to include corresponding accession numbers in the manuscript.

For papers reporting novel Macromolecular structures

Authors of papers describing structures of biological macromolecules must provide atomic coordinates and related experimental data (structure factor amplitudes/intensities for crystal structures, or restraints for NMR structures) upon request of editors for the purposes of evaluating the manuscript, if they are not already freely accessible in a publicly available and recognized database (for example,Protein DataBank,Uniprot,Nucleic Acids DatabaseorBiological Magnetic Resonance Databank). Electron microscopy-derived density maps and coordinate data must be deposited inEMDB.

Crystallographic data for small molecules

Manuscripts reporting new three-dimensional structures of small molecules from crystallographic analysis should include a .cif file and a structural figure with probability ellipsoids for publication as Supplementary Information. The structure factors for each structure should also be submitted. Both the strucure factors and the structural output must have been checked using the IUCR's CheckCIF routine, and a PDF copy of the output must be included at submission, together with a justification for any alerts reported. Crystallographic data for small molecules should be submitted to the Cambridge Structural Database and the deposition number referenced appropriately in the manuscript. Full access must be provided on publication.

Databases: The Cambridge Crystallographic Data Centre (CCDC) is appropriate for deposition of data on nucleosides, nucleotides and other small molecules.

A member site of theWorldwide Protein Data Bank:RCSB PDB,Protein Databank in Europe (PDBe),Protein Databank in Japan (PDBj), orBMRBis appropriate for deposition of data on proteins determined by X-ray crystallography and for all macromolecules determined by NMR methods.

The Nucleic Acid Database (NDB) is appropriate for atomic co-ordinate and structure factor data for crystal structures of nucleic acids. This can generally be handled by the Worldwide Protein Data Bank or RCSB Protein Data Bank described above.

NMR papers: Resonance assignments should be reported relative to DSS and not to HOD.

For papers reporting novel protein sequences

Protein sequences, which have been determined by direct sequencing of the protein, must be submitted toUniProt(i.e. TrEMBL, Swiss-Prot and PIR) using the interactive submission tool SPIN. Please note that they do not provide accession numbers, IN ADVANCE, for protein sequences that are the result of translation of nucleic acid sequences. These translations will forwarded automatically from the nucleotide sequence databases (EMBL/GebBank/DDBJ) and assigned UniProt accession numbers on incorporation into UniProt. Results from characterization experiments should also be submitted toUniProt: for novel sequences, these should be included with the sequence submission. Existing UniProt entries should also be updated. This can include information such as function, subcellular location, subunit, etc.

For papers reporting new ChIP-Seq data

New ChIP-Seq data must be deposited in GEO, with accession numbers at or before acceptance for publication.

Microarray data

All authors must comply with the'Minimal Information About a Microarray Experiment' (MIAME)guidelines published by the Microarray Gene Expression Data Society. NAR also requires submission of microarray data to the GEO or ArrayExpress databases, with accession numbers at or before acceptance for publication.

Quantitative PCR

Authors are encouraged to follow the'Minimal Information for Publication of Quantitative Real-Time PCR Experiments' (MIQE)guidelines, if appropriate. The guidelines are published by the Real-Time PCR Data Markup Language Consortium and can be found athttp://www.rdml.org/miqe.php

Other datasets

In addition to the above-mentioned mandatory requirements for data submission to community-endorsed public databases, Nature journals strongly recommend deposition of other types of data sets into appropriate public repositories that are at an earlier stage of development. Examples of such repositories that facilitate sharing large data sets, some of which can offer the option of anonymous referee access to data before publication, include: