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# Submission Guidelines

SUBMIT via our online manuscript submission system. If you need assistance, please contact the journal office at jem@rockefeller.edu or 212-327-8575.

## Presubmissions

Presubmission inquiries as to the suitability of a manuscript are welcome and can be via our online manuscript submission system. We typically respond within two days. Presubmission inquiries are intended for informal feedback on whether the scope of a manuscript is appropriate for JEM. Manuscripts will not be formally evaluated in full unless submitted via the usual process.

For authors interested in presubmission manuscript preparation support services, RUP suggests Editage. Use of this service is not mandatory for publication, does not guarantee peer review or acceptance, and you are not obliged to submit your manuscript to one of our journals if you choose to use the service.

## Preparing for submission to JEM

JEM accepts format-neutral first submissions. Manuscripts do not need to be formatted according to specific journal guidelines at this stage. To submit via our online system, you will need the following files and information:

### Manuscript

You may submit your manuscript as a single PDF or as separate files. Please ensure the title page includes all authors and affiliations. A full title, abstract, and short running title are required for submission. JEM accepts submission of Articles and Brief Definitive Reports. If you would like to submit a Review or Perspective for consideration, please contact the journal office directly at jem@rockefeller.edu.

### Cover letter

Authors should provide a cover letter describing the conceptual advance of their work, related or competing papers in press or consideration elsewhere, conflicts of interest, and whether submission is in response to a presubmission inquiry. Authors may request a specific editor, suitable reviewers, and up to three reviewer exclusions. If the original data in the manuscript are archived and accessible for review by editors and reviewers, please state this in your letter. If you would like the editors to consider peer reviewer comments from another journal, please include this information in your letter (as described in our Transfer policy). The cover letter will not be shared with reviewers.

### Corresponding author

The corresponding author is responsible for the integrity of all data and text described within the manuscript; archiving all data related to the manuscript and providing original data upon request; adherence to all journal policies, including disclosure of related work from all authors; appropriate author contribution descriptions and conflict of interest disclosures from all authors; getting approval from all authors for submission; and checking accuracy of the proofs. In some instances, it may be appropriate to have more than one corresponding author who would share the above responsibilities.

Even in cases of co-corresponding authors, one individual must be identified within our online manuscript submission system as the primary corresponding author. This individual will be the point of contact at all times with the JEM editorial and production offices and will be responsible for signing the license for publication agreement on behalf of all authors, appropriate materials and data sharing with the community after publication, and acting as arbiter in instances of author disputes.

### Funding and financial conflicts of interest

All authors must disclose any commercial affiliations or consultancies, stock or equity interests, or patent-licensing arrangements that could be considered a conflict of interest regarding the submitted manuscript. All conflicts of interest and sources of funding should be included in the Acknowledgments section of the manuscript.

## Revised submissions

Manuscripts invited to resubmit must be formatted according to all journal guidelines. General guidelines are included below. Detailed guidelines on figure and character limits based on article type can be found in our Manuscript types section. Authors should provide high-resolution individual figure files when they resubmit their revised manuscripts.

### Source Data

For manuscripts submitted on or after August 2, 2021, JEM requires authors to provide Source Data used to generate figures containing gels and Western blots. Source Data will be made available to reviewers during evaluation of revised manuscripts. Source Data will also be downloadable from the corresponding figures in the published article so that readers can reanalyze them or integrate them with other data.

Source Data consist of fully uncropped and unprocessed images for each gel/blot displayed in the main and supplemental figures. Files should be submitted using the Figure Source Data option in the manuscript submission system and should not be included as Supplemental Figure files. Authors should provide one Source Data file for each figure that contains gels and/or blots. File names for Source Data figures should be alphanumeric without any spaces or special characters (i.e., SourceDataF#, where F# refers to the associated main figure number or SourceDataFS# for those associated with Supplementary figures). The lanes of the gels/blots should be labeled as they are in the associated figure, the place where cropping was applied should be marked (with a box), and molecular weight/size standards should be labeled wherever possible.

#### Image Resolution and Size

Source Data Figures should be provided as individual PDF files (one file per figure). Authors should endeavor to retain a minimum resolution of 300 dpi or pixels per inch (ppi). Please review our instructions for export from PhotoshopIllustrator, and PowerPoint.

### Response to reviewers

Revised manuscript submissions must include a point by point response to the reviewer comments. The response file should detail how each reviewer remark was addressed experimentally and/or textually or why it could not be/was not addressed. The response to the reviewer comments file is shared with all reviewers. Authors may include data in their responses to the reviewers that they do not wish to include in the manuscript.

## Manuscript organization and formatting

### Title

The title should be less than 100 characters (including spaces). Make the title concise and accessible to a general readership.

### Authors

Full author names must be provided along with their institutional affiliations where the work was done. Names, affiliations, and author order should be checked carefully before resubmission. If a change of address is imminent for any author, indicate the change and the date effective. Corresponding author(s) must be identified with ORCID, email, and full mailing address.

### Summary

Provide a short, ~40-word summary statement for the online JEM table of contents and alerts. This summary should describe the context and significance of the findings for a general readership; it should be written in the present tense and refer to the work in the third person.

### Abstract

Abstracts must not exceed 160 words. The abstract should describe the relevant background, key results, and conceptual significance of the findings in a way that is accessible to a broad audience. Abstracts should not include references.

### Introduction

The Introduction should provide sufficient background to make the article accessible to non-expert readers; it should indicate what hypotheses were tested and provide sufficient context to make the significance of the problem studied and the rationale for the experiments clear to a broad audience.

### Results

The Results section describes the experiments performed and presents the findings observed. This section should be divided into subheadings. For Brief Definitive Reports, the Results and Discussion sections should be combined.

### Discussion

The Discussion summarizes the conclusions that can be drawn from the results, as well as the implications of the research. It should place your findings in the general context of the field and discuss any limitations of the experimental approaches you used. Subheadings may be used.

### Materials and methods

RUP journals are signatories of the NIH Reproducibility guidelines. There are no limits on the length of JEM materials and methods sections. JEM does not permit supplemental materials and methods. Materials and methods sections should be comprehensive and not simply reference a previous publication for details on how an experiment was performed. JEM does not permit citations of non–peer-reviewed publications or unpublished data in the Materials and methods section.

#### Reporting guidelines

We encourage all authors to utilize the EQUATOR network to identify appropriate reporting guidelines based upon study type. Authors should refer to the BRISQ reporting guidelines for any study in which human biospecimens are used. For authors reporting animal research, we encourage use of the ARRIVE guidelines. For studies using cell lines, authors should report the source of the line, whether the line has been authenticated and how, and the mycoplasma contamination status.

#### Reagents

All antibodies, cell lines, animals, and tools used in the manuscript should be described in full, including accession numbers for materials available in a public repository such as the Resource Identification Portal. For unique reagents such as antibodies, siRNA, primers, or other probes, authors should provide the full epitopes or sequences in the manuscript. Please list chemicals and scientific instruments used and their manufacturer.

#### Microscope image acquisition

The following information must be provided about the acquisition and processing of images: make and model of microscope; type, magnification, and numerical aperture of the objective lenses; temperature; imaging medium; fluorochromes; camera make and model; acquisition software; and any software used for image processing subsequent to data acquisition. Please include details and types of operations involved (e.g., type of deconvolution, 3D reconstitutions, and surface or volume rendering, gamma adjustments, etc.). If you export files from a microscope or other acquisition device, be sure to use consistent file formats (8 bit, 16 bit, etc.).

#### Statistical analysis

Authors should provide clear, detailed descriptions of their statistical analysis in the Materials and methods section and/or figure legends, including but not limited to the statistical test used, actual p-values, number of biological and technical replicates, measure of center, and measure of variability. If an editor or peer reviewer feels it necessary, we may request expert feedback specifically on statistical analysis within the manuscript.

### Supplemental material

Supplemental material is limited to figures, tables, large datasets, and videos. JEM does not permit supplemental text other than figure and video legends. A short summary paragraph of all supplemental material must appear at the end of the Materials and methods section.

### Author contributions

A separate author contribution section is required preceding the Acknowledgments in all research manuscripts. All authors should be mentioned and designated by their initials or full names. You may use either standard formatting (e.g., "AB designed and performed experiments") or the CRediT nomenclature.

### Acknowledgments

The Acknowledgments should recognize contributions from non-authors and disclose all funding sources and financial conflicts of interest. If there are no potential financial conflicts of interest, please add the following statement to the Acknowledgments section: "The authors declare no competing financial interests." (If potential conflicts are listed, the statement "The authors have no additional financial interests" should be added instead.)

### References

All in-text citations and references must be formatted according to the Reference guidelines. In-text citations should be Harvard style and listed alphabetically by the first author's last name in the Reference section. There is no limit to the number of references cited in a manuscript. JEM strongly encourages authors to cite the primary literature rather than review articles throughout their manuscripts.

JEM discourages citation of "data not shown," "manuscript in preparation," "manuscript submitted," etc., in any section of the manuscript. If included, "personal correspondence" must be accompanied by a signed letter of permission and may only be cited in the text.

Preprints may be cited in the text and included in the Reference section. Appropriate formatting is described in the JEM Reference guidelines. Note that citation of a previous preprint version of the manuscript under consideration should be included as a footnote.

### Abbreviations

A term that does not appear on the JEM standard abbreviations list must be used at least three times in a paper to qualify as an abbreviation. Spell out the term on first mention, and follow it with the abbreviated form in parentheses. Supply a list of nonstandard abbreviations used in the paper, in alphabetical order, giving each abbreviation followed by its spelled-out version.

### Figures

All submitted images must conform to the JEM Figure and Video Guidelines. Figures should be cited in numerical order in the text in the order they are mentioned. Figures should be prepared at publication size; whenever possible, figures will be reduced to a single-column width (85 mm). If you have any questions regarding figure preparation, please contact one of our in-house specialists at graphics@rockefeller.edu. All accepted figures will go through an image screening process prior to publication, as described in our Data integrity and plagiarism section.

### Videos

All submitted videos must conform to the Figure and Video Guidelines. Videos must be cited both in the Results section and in the legends of any figures that contain video stills or images related to the video. Videos are peer reviewed with the manuscript. A maximum of 10 videos may be posted for each article.

### Figure and video legends

All figures and videos must have titles and detailed legends. Figure legends should contain sufficient information that readers can understand what the data show without needing to refer back to the text. All symbols, such as arrows, must be defined in the legend. Scale bar measurements must be included in the legend. Where appropriate, legends should include any statistical test used, actual p-values, number of biological and technical replicates, measure of center, and measure of variability.

Each video legend should describe what is being shown, the cell type or tissue being viewed (including relevant cell treatments, concentration and duration, or transfection), the imaging method (e.g., time-lapse epifluorescence microscopy), what each color represents, how often frames were collected, the frames/second display rate, and the number of any figure that has related video stills or images.

### Tables

Include a table number and title for each table. Insert explanatory material and footnotes below the table, designating footnotes using lowercase superscript letters reading horizontally across the table. Supply units of measure at the heads of the columns. Abbreviations that are used only in a table should be defined in the table legend. Do not divide tables into subtables.

### Nomenclature

JEM follows the abbreviations and other conventions of Scientific Style and Format: The CSE Manual for Authors, Editors, and Publishers. For chemical nomenclature, follow the Subject Index of Chemical Abstracts. Capitalize trade names and give manufacturers' names. For drawing glycan structures using symbols, we recommend the Symbol Nomenclature for Glycans (SNFG) described in the 3rd edition of Essentials of Glycobiology and at the NCBI. Please include a citation in the methods section or in the legend of a figure using these symbols e.g, “Monosaccharide symbols follow the Symbol Nomenclature for Glycans (SNFG) (PMID 26543186, Glycobiology 25: 1323–1324, 2015; www.ncbi.nlm.nih.gov/glycans/snfg.html)”.

Gene names must be italicized. Authors must use the original name published for a gene unless they have obtained permission to rename the gene from the authors of the original study (or from a governing body such as, in the case of a yeast gene, the Saccharomyces Genome Database curator). Please follow the generally accepted rules for gene and protein nomenclature appropriate for the organism you are discussing. Gene nomenclature guidelines for humans (http://www.genenames.org/about/guidelines), rats and mice (http://www.informatics.jax.org/mgihome/nomen/gene.shtml), frogs (http://www.xenbase.org/gene/static/geneNomenclature.jsp), zebrafish (https://wiki.zfin.org/display/general/ZFIN+Zebrafish+Nomenclature+Guidelines), Drosophila (http://flybase.org/wiki/FlyBase:Nomenclature), C. elegans (http://www.wormbase.org/#012-34-5), and Arabidopsis (https://www.arabidopsis.org/portals/nomenclature/guidelines.jsp) are available at the indicated sites.

## Accepted manuscripts

Before we can accept your manuscript, the files and information below must be received by the editorial office.

### Manuscript files

High-resolution, editable, individual figure files are required, preferably in the original file format in which they were created. The manuscript text must be provided as a DOC or DOCX file.

A license to publish must be signed by the primary corresponding author prior to acceptance. View our license to publish agreement for more details.

### Permissions

If you are using previously published images in your manuscript, please see our permissions page for guidance.

### ORCID

RUP supports universal adoption of digital name identifiers to aid name disambiguation. ORCID identifiers are required of corresponding authors prior to publication and encouraged for all co-authors. You'll be prompted to provide ORCID identifiers by our submission software. Once ORCIDs are added to our system, they will be automatically populated for all future submissions. You can also use your ORCID to log in to our submission system. Your article will be automatically listed in your ORCID record upon publication. Learn more about ORCID and the benefits of registering here.

### Cover submissions

Authors whose manuscripts are accepted for publication may submit cover images and a brief legend for consideration. Images submitted should be at least 300 dpi at the size of publication (8.75" W x 11.25" H). Please submit cover suggestions via our online manuscript submission system when you upload final files prior to editorial acceptance.

### Graphical Abstract

Authors may include a Graphical Abstract with their manuscript. A Graphical Abstract is a single, concise, and self-explanatory visual summary of the main findings of the article that should capture the content of the article at a single glance. If provided, the Graphical Abstract will be available online only and will be used in all social media promotions to highlight the manuscript. Please follow our detailed instructions when creating your Graphical Abstract.

## Production and proofs

After acceptance, your manuscript will be sent to production for copy editing and preparation of the proofs. If you will be unavailable at any time while your manuscript is in production, please contact jem@rupress.org.

### Proofs

Corresponding authors will be emailed a link to proofs within two weeks after acceptance. Authors may choose to edit either the HTML or PDF versions of their proofs. Proofs must be returned within 48 hours.

### Daily publication

Articles are usually published within 48 hours after the author returns corrected proofs. This can vary depending on the extent of requested changes. Publication date also depends on whether the article has a companion article or press coverage.  On publication day, the articles are usually posted before 10AM EST. See our FAQ on daily publication for more details.

### Author fees

Authors will be charged a $2,000 flat fee for all publication charges. An author's inability to pay these charges will not affect the publication of acceptable manuscripts. Authors have the option to instead pay a single article charge of$5,300 in order to make their article open access immediately upon publication under CC-BY license.

### Reprints and journal copies

You will have the opportunity to order paper reprints of your article, print copies of the issue in which your manuscript will appear, or cover posters when you return your proofs.

Copyright of all material published in Rockefeller University Press journals remains with the authors. Unless immediate open access is selected, authors grant Rockefeller University Press an exclusive license to publish their work for the first six months. After six months, the work becomes available to the public to copy, distribute, or display under a Creative Commons Attribution-Noncommercial-Share Alike 4.0 International  license (CC-BY-NC-SA).

If immediate open acess is selected, upon publication the work becomes available to the public to copy, distribute, or display under a Creative Commons Attribution-Share Alike 4.0 International license (CC-BY).

## Appeals

Authors wishing to appeal an editorial decision should do so through the online manuscript submission system by clicking on the "Submit Appeal" link in the relevant manuscript record. A rebuttal letter and—if appropriate—a point by point response to the reviewers should be provided. A decision is usually communicated to the authors within 10 days. Please note that editors prioritize handling new submissions that have not yet received a first decision over appeals. JEM does not allow multiple appeals on a manuscript.

## Corrections and refutations

Corrections will be published at the discretion of the editors. Contact the journal office at jem@rockefeller.edu to request a correction to a published article.

JEM considers submissions aimed at refuting conclusions previously published in the journal. Such manuscripts should provide direct and definitive evidence that the conclusions in a previous JEM paper are incorrect. Please indicate in your cover letter that your manuscript is submitted as a refutation. The refutation will be peer reviewed, and the authors of the original work will be given the opportunity to submit a response for editorial consideration. Manuscripts that describe differing observations or draw different conclusions than past work through the use of new approaches or tools are a normal part of the scientific discourse and will not be considered as refutations. For more information, please contact the JEM editorial office at jem@rockefeller.edu.

JEM allows public commenting on all published articles using the Hypothesis annotation tool. Submitted comments should be constructive, factual, collegial, and relevant to the paper being discussed. Users must use their full name when posting comments. All comments are moderated by our editors prior to posting. Any content determined to be inappropriate will not be posted. Learn more about Hypothesis here.