GENERAL INFORMATION
Your chapter may include a Topic Introduction and/or
Protocols, as appropriate for your topic. The entire chapter
should not exceed 6000 words (excluding references),
and each section (i.e., each Topic Introduction and
Protocol) should not exceed 1500 words (see below).
Because your contribution will also be published online
in Cold Spring Harbor Protocols, each section must ‘stand
alone’ as described below. The text of the entire chapter
should be in one Word file, with the sections in the following
order:
- Topic Introduction, with its own abstract, references,
figures, tables, etc. (see below)
- Protocol(s), each with its own abstract, references,
figures, tables, etc. (see below)
Please submit your manuscript online by visiting
the submit page, entering your “Author
Area,” and clicking on “Accepted Commissions—
Papers
to be Submitted.” Once you’ve uploaded your manuscript,
we will send it to an Editor, who will contact you
within 4–6 weeks to request any revisions that may be
needed. After you have made appropriate changes, you
will upload your revised manuscript on the same site.
At this stage, your manuscript will be developmentally
edited by a one of our professional editors to ensure that
it follows our house style and format, and you may be
contacted if any clarifications/additions to your text are
required. You will have a final opportunity to check over
your contribution once you receive your page proofs.
TOPIC INTRODUCTION
The Topic Introduction should not exceed 1500 words
and include no more than 2 figures and tables. It should
provide background information on the topic. You may
compare different experimental approaches, outline
available resources, describe key features and considerations
of the methods, discuss applications for the
technique(s) presented in the detailed protocols later in
the chapter, and so forth. The introductory text should
be ‘stand alone’ (i.e., with its own title, list of references,
etc.) and include the following:
- Title page
- Title (this will be the chapter title as well as the
title of the Topic Introduction)
- Short title (50 characters and spaces) for running head
- List of authors and their affiliations (departments,
institutions, city, state/country, zip code)
- Corresponding author’s telephone number and
e-mail address
- Abstract (less than 250 words)
- Main text, including subheadings
- Acknowledgments
- References (see below)
- Figure legends (see below)
- Movie legends (see below)
- Tables
PROTOCOL(S)
Each protocol should not exceed 1500 words (excluding
references) and include no more than 1 figure and table.
If you are submitting more than one protocol, please
make sure that each protocol stands alone (i.e., has its
own abstract, references, figures, tables, etc.). The text
should be structured as follows:
- Title page (REQUIRED)
- Title of protocol
- Short title (50 characters and spaces) for running
head
- List of authors and their affiliations (departments,
institutions, city, state/country, zip code)
- Corresponding author’s telephone number and
e-mail address
- Abstract (less than 250 words; REQUIRED)
- Materials (REQUIRED)
This section has two subheads, as follows:
- Reagents (list all reagents and solutions alphabetically;
write out detailed recipes for solutions
that contain multiple ingredients [see below] and
identify these items by using the symbol after
the pertinent item in the Reagents list; include the
vendor and catalog number only if an item is unusual
or difficult to locate, or if the use of a specific
item is critical to the success of the procedure)
- Equipment (list all equipment alphabetically; it is
not necessary to list common items such as micropipettes
or gloves)
- Method (REQUIRED)
Write, in linear and numbered sequence, the steps
needed to perform the procedure. If desired, divide
the procedure into subsections, using subheadings
that correspond to major stages of the procedure. Include
supplementary information and alternative/optional
methods as notes. The text of each note should
be italicized and inserted below the step to which it
refers. Details should be provided, as follows:
- Always include working temperatures (e.g., cold
room, on ice, room temperature).
- When the precise timing of any portion of the procedure
is required, indicate this clearly. If appropriate,
indicate the approximate amount of time a given
step or steps should require.
- For centrifugation steps, specify time, temperature,
and speed (rpm or g). (Specify type of centrifuge
if providing instructions in rpm.) Always
state whether to discard/keep the supernatant/
pellet.
- For incubations, specify time, temperature, type
of incubator, and shaking (if necessary) in or on
what.
- For washes, specify conditions (e.g., temperature,
washing solution and volume, specific number of
washes, etc.).
- If the procedure can be interrupted at a step, say
so, and include appropriate storage conditions.
- At the end of the procedure, specify where any
products are to be used (e.g., cite another procedure)
and/or give long- or short-term storage conditions.
- Troubleshooting (OPTIONAL; only include this information
if available/appropriate)
Each troubleshooting point should be divided into
two parts:
- Problem (describe the problem and include the
step number at which the problem is detected)
- Solution (describe potential causes of the problem
and strategies for fixing them)
- Discussion (OPTIONAL; include as appropriate)
Discuss advantages, limitations, special considerations,
modifications, and applications of the technique.
Include examples (with figures and movies,
as appropriate). Acknowledge when the procedure is
derived from previous publications.
- Acknowledgments (OPTIONAL)
- References (REQUIRED; see below)
- Figure legends (OPTIONAL; see below)
- Movie legends (OPTIONAL; see below)
- Tables (OPTIONAL)
- Recipes (OPTIONAL; include as appropriate)
Write a detailed recipe for each solution or buffer in
the Reagents list (see above) that contains multiple
ingredients. When writing the recipes, consider the
following:
- Specify whether solution must be prepared fresh.
Include storage conditions (temperature and shelf
life) as appropriate.
- Specify which salt (e.g., phosphates, EDTA, etc.)
and hydration states should be used.
- Specify the final pH of the solution when appropriate.
- If autoclaving is necessary, specify time and psi.
- If H2O is required, specify distilled, double distilled,
sterile, etc.
- For aliquots, specify the size and number needed.
- For dilutions, specify number, degree of dilution,
and diluent.
- Include the vendor and catalog number only if a
reagent is unusual or difficult to locate, or if the use
of a specific reagent is critical to the success of the
procedure.
- Note that Cold Spring Harbor Protocols draws
from a common database of recipe information.
Because of this, the exact phrasing and names of
recipes and reagents may be altered in the developmental
editing process to better match items
already in the database.
REFERENCES
If you are using EndNote, please select the Genes and
Development style. Otherwise, to cite references in the
text, use the last name(s) of the author(s) and the year
(use first author's name and “et al.” for more than two authors). If more than one
paper is cited, place in chronological order (e.g., Smith
1994; Brown 1995; Jones et al. 1996). For citations of
unpublished work or personal communication, provide
names and first initials—for example, (P. Jones, unpubl.)
or (P. Jones, pers. comm.). These will not be listed in the
reference list, which is to contain only published work.
All references in the reference list should be arranged
alphabetically by the last name of the first author. Do not
use a numbered reference list or cite by number in the
text. See Sample Reference List below. Note that all authors should
be listed up to 10;if there are more than 10 authors, use "et al." after the 10th
name (see Proudfoot et al. 1993b below).
Sample Reference List
Ahnn J, Fire A. 1994. A screen for genetic loci required for body-wall
muscle development during embryogenesis in Caenorhabditis elegans.
Genetics 137: 483–498.
Ahringer J. 1991. “Post-transcriptional regulation of fem-3, a sex-determining
gene of C. elegans.” PhD thesis, University of Wisconsin,
Madison.
Barstead RJ, Waterston RH. 1991a. Vinculin is essential for muscle
function in the nematode. J Cell Biol 114: 715–724.
Barstead RJ, Waterston RH. 1991b. Cloning, sequencing, and mapping
of an a-actinin gene from the nematode Caenorhabditis elegans. Cell
Mobil Cytoskel 20: 69–78.
Chalfie M Jr, Thomson JN, Sulston JE. 1983. Induction of neuronal
branching in C. elegans. Science 221: 61–63.
Fischmann DA, Vaughn K, Weber F, Einheber S. 1991. Myosin binding
proteins: Intracellular members of the immunoglobulin super
family. In Frontiers of muscle research: Muscle contraction and muscle
dystrophy, 2nd ed. (ed. E Ozawa et al.), pp. 211–222. Elsevier,
Amsterdam.
Gerhart J. 1980. Mechanisms regulating formation in the amphibian
egg and early embryo. In Biological regulation and development (ed.
RF Goldberger), Vol. 1, pp. 133–316. Plenum, New York.
Johnson J. 2000. The mouse. In Proceedings of the Tenth Annual Meeting
of Mouse Genetics, p. 83. Jackson Laboratory, Bar Harbor, ME.
Komissarova N, Kashlev M. 2011. Arrest of transcription: Escherichia
coli RNA polymerase translocates backward, leaving the 3' end of
the RNA intact and extruded. Proc Natl Acad Sci (in press).
Levesque M. 2007. A microRNA feedback circuit in midbrain dopamine
neurons. PloS ONE 2: e1227. doi: 10.1371/journal.pone/0001227.
Proudfoot L, Kusel JR, Smith HV, Kennedy MW. 1993a. External stimuli
and intracellular signalling in the modification of the nematode
surface during transmission to the mammalian host environment.
Parasitology 107: 556–559.
Proudfoot LJ, Kusel JR III, Smith HV, Hanett W, Worms MJ, Kennedy
MW, Johnson AB, Thomas E, Lin X, Corbett K, et al. 1993b. Rapid
changes in the surface of parasitic nematodes during transition
from pre- to post-parasitic forms. Parasitology 107: 107–117.
Sive HL, Grainger M, Harland RM. 2000. Early development of Xenopus
laevis: A laboratory manual. Cold Spring Harbor Laboratory Press,
Cold Spring Harbor, NY.
LEGENDS FOR FIGURES, MOVIES, AND TABLES
Legends should start with a short title that describes what
is shown. The remainder of the legend should be as brief as
possible and should not contain experimental detail. Parts
of figures should be labeled with capital letters (e.g., A, B,
and C). Please indicate clearly if the figure, table, or movie
was taken from elsewhere (e.g., reprinted or modified) and
obtain permission to republish (see below).
FIGURES
- We can only accept your electronic art as an EPS or
TIFF file. Virtually all common artwork programs
are capable of saving files in these formats. These options
can normally be found under the ‘Save As…’ or
‘Export…’ commands in the ‘File’ menu. (See specific
instructions below on saving your files in the most common
programs.)
- All images should be saved in CMYK (color), grayscale
(halftones), or bitmap (black and white line art)
mode. Please note that images supplied in color will
sometimes appear in black and white in print due to
the additional costs involved in color printing. Please
do a test to make sure your color images will also produce
nicely in black and white.
- Image resolution is critical to the clarity and sharpness
of the final printed piece. Image resolution should be
set at 300 DPI for color and grayscale artwork. All
line art (bitmap images) should be 1200 DPI. When
supplying images please make sure the files are at the
correct resolution. Any figures that do not meet the
above requirement are subject to being returned for a
better quality image.
- Use Helvetica postscript font in point sizes no smaller
than 6 pt type and no larger than 10 pt type. Optimum
point size for type in artwork is 8 pt. Please make
sure all fonts are embedded in the image. CSHL Press
strives to make all artwork look consistent online and
in printed form. In order to achieve this consistency, it
is important to use the Helvetica postscript font as well
as follow the directions below for creating your artwork
(see Creating Your Artwork).
- If your figure has multiple parts (more than one image
in the figure), please make sure the part labels (A, B,
C, D) are 9 pt Helvetica bold, cap.
- Authors may mail a print of their artwork if they are
concerned that elements might not convert accurately
during production.
- Please make sure that your files are properly labeled by
figure number and format (e.g., Fig_1.tif or Fig_2.eps).
- Upload only final art files that have been carefully proofread.
Do not embed figure legends in the art files. All
figure legends should be placed at the end of the manuscript.
DO NOT EMBED FIGURES WITHIN THE
TEXT FILES. For example, figures should not be embedded
in a Word file. The figures should be separate files.
Saving Files in Illustrator and Photoshop
Adobe Illustrator
- Under the File menu, choose save as, format (Illustrator
EPS).
- Click save and a window comes up.
- Save as “Illustrator EPS.”
- Under options, click include document fonts, click include
document thumbnails.
- Preview should be checked as 8-bit Macintosh.
- Click okay.
- In case we have trouble with your file, please download
all fonts on the disk that were used in creating
your artwork.
The pre
view box is very important. Make sure it is
checked off as 8-bit Macintosh.
If your artwork is in 4-color, please make sure you create
the artwork using CMYK (not RGB) colors.
Adobe Photoshop
- Under the File menu, choose save as, format (TIFF).
- Click save.
- Under TIFF options check Macintosh; do not check
LZW compression.
- Click okay.
If your artwork is in 4-color, please make sure you create
the artwork using CMYK colors (not RGB or Pantone
colors). Please make sure the resolution is at 300 dpi.
Creating Your Artwork
- Please submit your illustrations as Adobe Illustrator
EPS files.
- Please create your artwork at exact size. Artwork
should not be larger than the measurements noted
below.
• 8 ½ x 10 7/8'' trim size, single column layout: no
larger than 5 3/4'' wide and 8'' long. Can go up to 7''
wide if necessary but we prefer the artwork to stay
in column width. Please try, whenever possible, to
keep the figure size to 1/2 or 1/3 of the page size.
- All labels should be set in Helvetica postscript font.
Optimum point size for labels should be 8 pt. Type
sizes can vary but should range no smaller than 6 pt
type and no larger than 10 pt type unless you feel it
is necessary to the meaning of the artwork. Labels
should be in sentence case.
- Part labels (A, B, C, D) should be 9 pt. Helvetica
bold, cap.
- All fonts should be embedded in the file.
- Line widths (as well as dotted lines and lines with
arrows) should be .5 pt to .75 as the basic line weight
for drawing, with heavier or lighter line weights for
emphasis.
- If you are bringing TIFF images into Illustrator,
make sure “include placed files” is checked in the
options box.
- When creating tints (shades of black or color),
please make sure you do not go above 15% when
type is placed over the tinted area (unless the text is
knocked out to white). All color artwork should be
created in cmyk mode.
- Color choices should be harmonious throughout.
There should be consistency of color choice, tone, density,
and hue for each article. Avoid the use of “neon”
colors. No color panels should be used for backgrounds.
Shading and highlighting should be subtle.
- Overprint black ink to aid in registration. Because
black ink is opaque (and usually the last to be printed),
it doesn’t look much different when printed over
a color as opposed to a white background. Overprinting
black can prevent gaps from appearing between
black and colored areas of your artwork. Under the
help menu in Illustrator, directions for implementing
overprinting are clearly explained.
MOVIES
Preferred movie formats are QuickTime (.mov) and
Flash (.flv or f4v). Files should have a maximum width
of 450 pixels and a maximum height of 400 pixels, but
the appropriate dimensions depend on the proportions
of the image. Movies should be cited in the text where
appropriate.
TABLES
Please supply all tables in Word format (not as figures/
images). Small tables that are critical to the Method section
of a protocol (e.g., steps of a PCR program) should be
included within the Method steps themselves (see above)
and need not be numbered/cited. All other tables should be
numbered and cited in the text as appropriate.
PERMISSIONS
It is your responsibility to obtain permission from the
copyright holder to reproduce or modify any figure or
table that has been previously published and include a
copy of the permission with your manuscript files upon
acceptance for publication. Note that we need both print
and non-print (online) media rights. The figure, table, or
movie legend should contain the following information:
“Reprinted [or Modified], with permission, from author,
year. Copyright publisher.” The complete reference must
also 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 conflict of interest or competing
financial interest that may be perceived as contributing
to potential bias. Examples include employment by or
stocks or shares in, one or more organizations that may
be financially affected by the publication of a paper, as
well as patents or patent applications whose value may
be affected by the publication of the paper.
Protection of Human Subjects and Animals in Research
Where data from experiments involving animals or human
subjects are shown, authors must demonstrate that
these were in accordance with the ethical standards of
the relevant institutional and national committees for
such matters.
Informed Consent Where identifying information,
such as patients’ names, initials, or hospital numbers, is
shown, authors must demonstrate that the patient (or
parent or guardian) has given written informed consent
for publication and been shown the manuscript prior to
publication.
Attribution and Plagiarism Authors are asked to ensure
that previously published work is appropriately
acknowledged and cited correctly. Where statements
made in previously published work are reproduced verbatim,
this must be indicated by the use of quotation
marks (“”), and an accompanying reference must be
provided. Cold Spring Harbor Laboratory Press reserves
the right to employ automated tools to identify any instances
of plagiarism and withdraw the contribution if
this is detected.
CSH Protocols Instructions for Authors