Cold Spring Harbor Protocols Instructions for Authors

For presubmission inquiries, please e-mail the editors. Protocols should be submitted through the electronic manuscript processing system available here.

Authors: Please follow the guidelines below when preparing your protocol for submission. The strict formatting provided must be adhered to in order to meet publication requirements. Submit text as a Microsoft Word document.

Overall length: 2-6 printed pages, or 1000-3000 words.

Title: Titles should not exceed 20 words. Please include in titles any terms likely to increase search results.

Source: Author name(s) and affiliation(s).

Introduction: Approximately 150-200 words; should be a brief summary of the technique's principles and scope. The Introduction will be deposited into Medline as the Abstract; therefore, citations to other work should not be included in this section. Additional information may be included in the Discussion.

Related Information: Indicate Figures, large informational Tables, Movies, Topic Introductions, and Information Panels to which the protocol should be linked. See below for a description of each file type; include each additional file separately with your submission. Links to other protocols, if any, may also be included in this section.

Materials: Alphabetical listing of all reagents and solutions as well as specialized, non-standard equipment, including full product details and manufacturers' names. Where necessary, include the quality grade of reagents used. Please include and highlight all cautions, followed by [open angled bracket]![close angled bracket], as well as all recipes [open angled bracket]R[close angled bracket], using the symbols following the pertinent item as necessary (use angled brackets to surround ! or R instead of parentheses). Include a full-text description of cautions and recipes at the end of the protocol. Note that CSH Protocols articles draw from a common pool of recipe and caution information. Because of this, the exact phrasing and names of recipes, cautions and reagents may be altered in the post-acceptance editing process to better match items already in our database. Organize materials under only two subheadings:

Method: Briefly describe, in linear and numbered sequence, the precise instructions to perform the action required. Divide the procedure with subheadings (fewer than 8 words) corresponding to major stages of the process. The numbering of steps should be continuous from one stage to the next. Note that each step is limited to one paragraph.

Troubleshooting: These notes are comprehensive and are divided into two sections: Problem and Solution. Each Problem should have a distinct Solution, and there is no limit to the number of Problems included. Keep descriptions for each section brief. Each Problem should be listed with an appropriate step number; this step number should indicate the stage at which the problem is detected, not created.

Discussion: Consider advantages, limitations, and special considerations of the technique. Discuss use for various applications in comparison to alternative techniques and/or provide specific examples (if applicable) and cross-reference to the Method section. Limit the Discussion to 1-2 paragraphs and include citations where appropriate.

Acknowledgments: Include any acknowledgments here, as briefly as possible.

References: Include key reviews and/or a hypothesis-driven paper in which the technique has been used. Brief citations in the text should correspond to full references in the list.

NOTE: Only those articles that are published or are in press will be included in References. The Reference list should be presented in alphabetical order. ALL authors' names up to 10 before et al. should be included. Unpublished data, submitted manuscripts (noted as "in prep."), or personal communications should appear in text only (not in References) and should include first initials and last names of authors (again, up to 10 before et al.). References are name/date citations in text. Reference examples (for style only) are:

Pavio A, Scharf S, Horn GT. 1975. Perceptual comparisons through the mind's eye. Mem Cognit 3: 635-647.

Sampath P, Mazumder B, Seshadri V, Gerber CA, Chavatte L, Kinter M, Ting SM, Dignam JD, Kim S, Driscoll DM, et al. 2004. Noncanonical function of glutamyl-prolyl-tRNA synthetase: Gene-specific silencing of translation. Cell 119: 195–208.

Strunk W, White EB. 1979. The elements of style. Macmillan, New York, NY.

Tymowska J. 1991. Polyploidy and cytogenetic variation in frogs of the genus Xenopus. in Amphibian cytogenetics and evolution (eds. DM Green and SK Sessions), pp. 259-297. Academic Press, San Diego, CA.

For the following sections please provide as separate Word documents, as they will be linked to and from the protocol rather than included within the protocols (with one exception to this in Figures).

Figures: Figures that illustrate the technique, example results, etc. are welcome and should include accompanying legends. Figures must be provided as separate files according to the Digital Art Guidelines. Include figure legends with the manuscript following the References section. If possible, include a flow-chart diagram that illustrates the procedure or a figure that illustrates its application (see Digital Art Guidelines for acceptable file formats).

Tables: Small tables that are critical to the Method section should be included within the protocol steps. (All tables must be created using MS Word's table format, which can be found from MS Word's Table pull-down menu. Do not 'tab over' to align columns visually, giving the appearance of a table.) Informational tables providing background or alternative material that may pertain to one or more protocols should be included as Information Panels and linked to and from the Related Information section and/or a link from within the appropriate step.

Movies: In the Related Information section, indicate that a movie is available, and include the movie's title and/or give a description. The movie may also be cited at the appropriate protocol step, if desired.

Math Objects: Before submitting your Word file, please make sure to UPDATE any MathType objects in the file; otherwise, italics and other font specs might be lost. Greek symbols should be inserted directly from Word's "symbol insert" pulldown menu; equations/schemes should be inserted using MathType or Word's Equation Editor. (Note: Authors who run Word 2007 also are requested to create equations using MathType or Word's original Equation Editor. Equations that are created in Word 2007's Equation Builder are converted to picture formats, which should be avoided.)

Other Article Types:

Topic Introduction: This material usually pertains to more than one protocol and provides general and background information, theory, and applications about the technique(s) to which it is linked. Please reference Topic Introductions in the Related Information section(s) and provide these documents as separate MS Word files.

Information Panels: These articles provide functional and/or practical information about a particular topic that is in a protocol, but they do not contain either information that is critical to performing the method or historical, encyclopedic-type background details. Please reference Information Panels in the Related Information section(s) and provide these documents as separate MS Word files. Information Panels may contain figures, tables, and movies.

Emerging Model Organisms: See full instructions here.

CSH Protocols encourages authors to submit Topic Introductions and Information Panels in conjunction with protocols, but we recommend that authors contact the CSH Protocols editors via presubmission inquiry to determine the suitability of these documents. All Topic Introductions and Information Panels will be peer-reviewed along with the protocols to which they are linked.

Permissions: It is your responsibility to obtain permission (from both the publisher and the author) to reproduce or modify any figure or table that has been previously published and include a copy of the permission upon acceptance for publication. A sample permission request letter can be found here. The figure or table legend should contain the following information: (Reprinted [or Modified], with permission, from author, year. Copyright publisher.) and complete reference must appear in the Reference List. Authors must also obtain permission to reprint material from websites from the Web Master of that site.

Ethics:

Conflicts of Interest: Upon acceptance, each author is required to declare any conflicts of interest or competing financial interests that may be perceived as contributing to potential bias. Examples would be funding for a research program or employment by or stocks or shares in one or more organizations that may be financially affected by the publication of this paper, as well as patents or patent applications whose value may be affected by the publication of this paper.

Protection of Human Subjects and Animals in Research: For techniques requiring human subjects, authors must include a notice that informed consent of subjects should be obtained as per the standards of the relevant national or institutional committee. Any protocols requiring the use of human subjects or animals must include a notice stating that the researcher must seek approval for these procedures from the appropriate national or institutional review committees for such matters.