Cold Spring Harbor Protocols

Publisher: Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press

Journal description

Cold Spring Harbor Laboratory is renowned for its teaching of biomedical research techniques. For decades, participants in its celebrated, hands-on courses and users of its laboratory manuals have gained access to the most authoritative and reliable methods in molecular and cellular biology. Now that access has moved online. Cold Spring Harbor Protocols is a definitive, interactive source of new and classic research techniques. The database is fully searchable by keyword and subject, and it has many novel features - such as discussion forums and personal folders - made possible by online publication. Its coverage includes cell and molecular biology, genetics, bioinformatics, protein science, and imaging. Protocols are presented step-by-step and edited in the style that has made Molecular Cloning, Antibodies, Cells and many other CSH manuals essential to the work of scientists worldwide. Protocols will be continuously expanded, updated, and annotated by the originators and users of the techniques. CSH Protocols - continuing Cold Spring Harbor Laboratory's 60-year tradition as a source of trusted techniques.

Current impact factor: 4.63

Impact Factor Rankings

Additional details

5-year impact 0.00
Cited half-life 6.30
Immediacy index 0.75
Eigenfactor 0.18
Article influence 1.46
Website Cold Spring Harbour Protocols website
Other titles CSH protocols, Protocols, CSH protocols, CSH protocols online
ISSN 1559-6095
OCLC 62938806
Material type Document, Periodical, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

Cold Spring Harbor Laboratory Press

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Author's pre-print on preprint server
    • Author's pre-print must be updated with citation, DOI and link to article upon publication
    • Publisher's version/PDF may be used after 6 months
    • Publisher's version/PDF and Author's post-print on author's personal website, institutional repository, funder's designated repository
    • Authors retain copyright
    • Content automatically sent to PubMed Central after 6 months
    • Publisher copyright and source must be acknowledged
    • Publisher last contacted on 15/07/2013
  • Classification
    green

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Protein-DNA interactions are responsible for numerous critical cellular events: For example, gene expression and silencing are mediated by transcription factor protein binding and histone protein modifications, and DNA replication and repair rely on site-specific protein binding. Chromatin immunoprecipitation (ChIP) is the only molecular assay that directly determines, in a living cell, the binding association between a protein of interest and specific genomic loci. It is an indispensible tool in the biologist's toolbox, but the many limitations of this technique prevent broad adoption of ChIP in biological studies. The typical ChIP assay can take up to 1 wk to complete, and the process is technically tricky, yet tedious. The ChIP assay yields are also low, thus requiring on the order of millions to billions of cells as starting material, which makes the assay unfeasible for studies using rare or precious samples. For example, fluorescence-activated cell sorting (FACS) of cancer stem cells (CSCs) obtained from primary tumors, rarely yields more than ~100,000 CSCs per tumor. This protocol describes a microfluidics-based strategy for performing ChIP, which uses automation and scalability to reduce both total and hands-on assay time, and improve throughput. It allows whole fixed cells as input, and enables automated ChIP from as few as 2000 cells.
    No preview · Article · Dec 2015 · Cold Spring Harbor Protocols
  • [Show abstract] [Hide abstract]
    ABSTRACT: This protocol is designed for large-scale isolation of highly purified peroxisomes from Saccharomyces cerevisiae using two consecutive density gradient centrifugations. Instructions are provided for harvesting up to 60 g of oleic acid-induced yeast cells for the preparation of spheroplasts and generation of organellar pellets (OPs) enriched in peroxisomes and mitochondria. The OPs are loaded onto eight continuous 36%-68% (w/v) sucrose gradients. After centrifugation, the peak peroxisomal fractions are determined by measurement of catalase activity. These fractions are subsequently pooled and subjected to a second density gradient centrifugation using 20%-40% (w/v) Nycodenz. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Sep 2015 · Cold Spring Harbor Protocols
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    ABSTRACT: Because core facilities that generate transgenic founder mice for a reasonable fee are now available at most major research institutions, generating new Thy1-XFP transgenic animals (in which XFP stands for any fluorescent protein) is an option even for relatively small laboratories. Here, we provide a protocol for screening offspring of Thy1 transgenic founders. Acute neuromuscular explants are obtained from 3-wk-old F1 mice that have been produced by crossing Thy1 transgenic founders and commercially obtained inbred mice. Thy1-driven expression is detected by fluorescence microscopy. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Sep 2015 · Cold Spring Harbor Protocols
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    ABSTRACT: Total internal reflection fluorescence microscopy (TIRFM) is a wide-field illumination technique that illuminates only the molecules near the glass coverslip. It has become widely used in biological imaging because it has a significantly reduced background and high temporal resolution capability. The principles of TIRFM are illustrated in this protocol, in which the movements of motor proteins are imaged as they move along microtubules within live axonemes. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Sep 2015 · Cold Spring Harbor Protocols
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    ABSTRACT: In this protocol, colon cancer is induced in mice through a series of injections with 1,2-dimethylhydrazine. Mice will develop primarily colon tumors starting at about 3 mo after the first injection. Tumors in the lung, uterus, and small intestine may also be seen, as well as lymphomas. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Sep 2015 · Cold Spring Harbor Protocols
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    ABSTRACT: This protocol describes the isolation of peroxisomes from Saccharomyces cerevisiae by density gradient centrifugation using a sucrose, OptiPrep, or OptiPrep/sucrose gradient. Oleic acid-induced cells are first converted to spheroplasts using lyticase for cell wall digestion. Spheroplasts are homogenized, and nuclei and cell debris are removed by low-speed centrifugation to produce a postnuclear supernatant (PNS). Separation of the PNS by density gradient centrifugation is suitable for many analytical applications; however, to increase the yield of peroxisomes, further fractionation of the PNS is possible. Differential centrifugation of the PNS allows removal of the cytosol and other contaminating organelles, resulting in an organellar pellet (OP) enriched in peroxisomes and mitochondria that can be loaded onto the density gradient. Following density gradient centrifugation of the PNS or OP, fractions are collected from the bottom of the centrifuge tube. The distribution of organelles, including peroxisome peak fractions, is characterized by measurement of marker enzyme activity. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Sep 2015 · Cold Spring Harbor Protocols
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    ABSTRACT: It is often desirable to have cellular DNA on hand. DNA is stable and can be maintained intact for many years. This protocol describes the preparation of DNA from nuclei after the cytoplasmic extract has been removed. The resulting DNA is suitable for polymerase chain reactions and Southern blots to determine copy number and sites of integration of plasmids in stable cell lines. Quantitation of DNA may not be exact because RNA is not completely removed. The method can also be used on whole cells, but there will be more RNA contamination. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Sep 2015 · Cold Spring Harbor Protocols
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    ABSTRACT: In this protocol, urethane (ethyl carbamate) is used to induce lung tumors in mice. The use of urethane as an experimental carcinogen is especially attractive as it is inexpensive, relatively safe to handle, stable, and water soluble, and the protocol involves simple intraperitoneal (i.p.) injections in young mice. Urethane typically induces bronchioalveolar adenomas and, to a lesser extent, adenocarcinomas that resemble the adenocarcinoma subtype of non-small cell lung carcinoma. On a sensitive genetic background such as A/J, mice develop multiple adenomas visible on the lung surface by 25 wk, followed by the appearance of adenocarcinomas by 40 wk. Less-sensitive strains such as B6/129 develop tumors with a longer latency. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Sep 2015 · Cold Spring Harbor Protocols
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    ABSTRACT: The goal in fluorescence microscopy is to detect the signal of fluorescently labeled molecules with great sensitivity and minimal background noise. In epifluorescence microscopy, it is difficult to observe weak signals along the optical axis, owing to the overpowering signal from the out-of-focus particles. Confocal microscopy uses a small pinhole to produce thin optical sections (∼500 nm), but the pinhole rejects some of the in-focus photons as well. Total internal reflection fluorescence microscopy (TIRFM) is a wide-field illumination technique that illuminates only the molecules near the glass coverslip. It has become widely used in biological imaging because it has a significantly reduced background and high temporal resolution capability. TIRFM has been used to study proteins in vitro as well as signaling cascades by hormones and neurotransmitters, intracellular cargo transport, actin dynamics near the plasma membrane, and focal adhesions in living cells. Because TIRF illumination is restricted to the glass-water interface and does not penetrate the specimen, it is well suited for studying the interaction of molecules within or near the cell membrane in living cells. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Sep 2015 · Cold Spring Harbor Protocols
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    ABSTRACT: Peroxisomes are multifunctional, dynamic organelles present in nearly all eukaryotic cells. Determining their structural and functional characteristics often requires obtaining isolated and purified peroxisomes via subcellular fractionation. Subcellular fractionation techniques are generally based on a three-step procedure: preparation of a cell-free homogenate (postnuclear supernatant), generation of an organellar pellet by differential centrifugation, and density gradient centrifugation. Here we introduce methods for small-scale isolation of peroxisomes from yeast cells using different gradient media as well as large-scale purification using a two-step gradient centrifugation. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Sep 2015 · Cold Spring Harbor Protocols
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    ABSTRACT: New generations of Thy1-XFP transgenic mice (where XFP stands for any fluorescent protein) can now be readily generated, given the availability of core facilities or commercial providers of Thy1 pronuclear injections. Here, we provide a protocol for screening founder progeny. Transcardial perfusion is performed on 3-wk-old F1 mice that have been produced by crossing Thy1 transgenic founders and commercially obtained inbred mice. Cryosections are generated, and Thy1-driven expression is detected by histological characterization. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Sep 2015 · Cold Spring Harbor Protocols
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    ABSTRACT: Ca(2+) uncaging can be used to create a spatially homogenous elevation of the intracellular free Ca(2+) concentration, [Ca(2+)]i, in cells. When applied to nerve terminals or secretory cells, this technique allows one to elicit transmitter release with a [Ca(2+)]i signal of measurable amplitude, and therefore to directly relate the rate of transmitter release to the measured [Ca(2+)]i. When combined with patch-clamp measurements, Ca(2+) uncaging is done by introducing a Ca(2+)-loaded photolyzable Ca(2+) chelator (like DM-nitrophen) into the cell via the whole-cell patch-pipette. A brief light pulse from a flash lamp or a pulsed laser is used to photolyze the DM-nitrophen. The resulting increase in [Ca(2+)]i is measured with ratiometric fluorescent indicators of suitable Ca(2+) affinity, such as Fura-2, Fura-4F, Fura-2FF, or Fura-6F, depending on the postflash [Ca(2+)]i values. To quantitatively measure [Ca(2+)]i, an accurate calibration of the fluorescent indicator in the presence of the photolyzable Ca(2+) chelator is necessary, which will be described here. Ca(2+) uncaging in nerve terminals has proven useful for investigating Ca(2+)-dependent functions like transmitter release, short-term plasticity, and exocytosis-endocytosis coupling in the presynaptic compartment of neurons. © 2015 Cold Spring Harbor Laboratory Press.
    No preview · Article · Aug 2015 · Cold Spring Harbor Protocols