Abstract:
:Chromatin and transcriptional processes are among the most intensively studied fields of biology today. The introduction of chromatin immunoprecipitations (ChIP) represents a major advancement in this area. This powerful method allows researchers to probe specific protein-DNA interactions in vivo and to estimate the density of proteins at specific sites genome-wide. We have introduced several improvements to the traditional ChIP assay, which simplify the procedure, greatly reducing the time and labor required to complete the assay. The simplicity of the method yields highly reproducible results. Our improvements facilitate the probing of multiple proteins in a single experiment, which allows for the simultaneous monitoring of many genomic events. This method is particularly useful in kinetic studies where multiple samples are processed at the same time. Starting with sheared chromatin, PCR-ready DNA can be isolated from 16-24 ChIP samples in 4-6 h using the fast method.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Nelson JD,Denisenko O,Bomsztyk Kdoi
10.1038/nprot.2006.27subject
Has Abstractpub_date
2006-01-01 00:00:00pages
179-85issue
1eissn
1754-2189issn
1750-2799pii
nprot.2006.27journal_volume
1pub_type
杂志文章相关文献
Nature Protocols文献大全abstract::Isolated protoplasts serve as a transient expression system that is highly representative of stable transgenics in terms of transcriptome responses. They can also be used as a cellular system to study gene transactivation and nucleocytoplasmic protein trafficking. They are particularly useful for systems studies in wh...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.147
更新日期:2014-09-01 00:00:00
abstract::Fast, high-resolution mapping of heterogeneous interfaces with a wide elastic modulus range is a major goal of atomic force microscopy (AFM). This goal becomes more challenging when the nanomechanical mapping involves biomolecules in their native environment. Over the years, several AFM-based methods have been develop...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-018-0070-1
更新日期:2018-12-01 00:00:00
abstract::The bimolecular fluorescence complementation (BiFC) assay is a powerful tool for visualizing and identifying protein interactions in living cells. This assay is based on the principle of protein-fragment complementation, using two nonfluorescent fragments derived from fluorescent proteins. When two fragments are broug...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2008.16
更新日期:2008-01-01 00:00:00
abstract::Here, we provide comprehensive, highly efficient protocols for Agrobacterium tumefaciens-mediated transformation of a wide range of rice genotypes. Methods that use either immature embryos (japonica and indica rice) or calli (japonica cultivars and the indica cultivar, Kasalath) as a starting material for inoculation ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2008.46
更新日期:2008-01-01 00:00:00
abstract::This protocol describes a general method for the preparation of RNAs in which the reactivity or hydrogen-bonding properties of the molecule are modified in a photoreversible fashion by use of a caging strategy. A single caged adenosine, modified at the 2' position as a nitro-benzyl ether, can be incorporated into shor...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.154
更新日期:2007-01-01 00:00:00
abstract::Here we describe a protocol for advanced CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis). The CUBIC protocol enables simple and efficient organ clearing, rapid imaging by light-sheet microscopy and quantitative imaging analysis of multiple samples. The organ or body is cleared by im...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2015.085
更新日期:2015-11-01 00:00:00
abstract::This protocol provides a detailed procedure for the chemical synthesis of proteins through native chemical ligation of peptide hydrazides. The two crucial stages of this protocol are (i) the solid-phase synthesis of peptide hydrazides via Fmoc chemistry and (ii) the native chemical ligation of peptide hydrazides throu...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.152
更新日期:2013-12-01 00:00:00
abstract::AMPylation (adenylylation) has been recognized as an important post-translational modification that is used by pathogens to regulate host cellular proteins and their associated signaling pathways. AMPylation has potential functions in various cellular processes, and it is widely conserved across both prokaryotes and e...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2015.044
更新日期:2015-05-01 00:00:00
abstract::Competition chromatin immunoprecipitation (competition ChIP) enables experimenters to measure protein-DNA dynamics at a single locus or across the entire genome, depending on the detection method. Competition ChIP relies on a cell containing two copies of a single DNA-associated factor, with each copy of the factor di...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.077
更新日期:2013-01-01 00:00:00
abstract::Generation of precisely patterned neural cells from human pluripotent stem cells (hPSCs) is instrumental in developing disease models and stem cell therapies. Here, we provide a detailed 16-d protocol for obtaining high-purity ventral midbrain (VM) dopamine (DA) progenitors for intracerebral transplantation into anima...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2017.078
更新日期:2017-09-01 00:00:00
abstract::We outline current in vitro and in vivo models for experimental proliferative vitreoretinopathy (PVR) and provide a detailed protocol of our standardized in vivo PVR model. PVR is the leading cause of failed surgical procedures for the correction of rhegmatogenous retinal detachment. The pathogenesis of this multifact...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.4
更新日期:2007-01-01 00:00:00
abstract::Iterative saturation mutagenesis (ISM) is a new and efficient method for the directed evolution of functional enzymes. It reduces the necessary molecular biological work and the screening effort drastically. It is based on a Cartesian view of the protein structure, performing iterative cycles of saturation mutagenesis...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.72
更新日期:2007-01-01 00:00:00
abstract::An important area of proteomics involves the need for quantification, whether relative or absolute. Many methods now exist for relative quantification, but to support biomarker proteomics and systems biology, absolute quantification rather than relative quantification is required. Absolute quantification usually invol...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.129
更新日期:2006-01-01 00:00:00
abstract::We describe a protocol for easy isolation and culture of human umbilical vein endothelial cells (HUVECs) to supply every researcher with a method that can be applied in cell biology laboratories with minimum equipment. Endothelial cells (ECs) are isolated from umbilical vein vascular wall by a collagenase treatment, t...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.54
更新日期:2007-01-01 00:00:00
abstract::Unlike transplantation of other solid organs, vascularized mouse lung transplantation has only recently been developed. In this protocol, we describe a detailed method for performing a vascularized and aerated mouse orthotopic lung transplant, which to date represents the most physiological mouse model of lung transpl...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2008.218
更新日期:2009-01-01 00:00:00
abstract::Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-019-0265-0
更新日期:2020-02-01 00:00:00
abstract::Top-down proteomics (TDP) by mass spectrometry (MS) is a technique by which intact proteins are analyzed. It has become increasingly popDesalting and concentrating GELFrEEular in translational research because of the value of characterizing distinct proteoforms of intact proteins. Compared to bottom-up proteomics (BUP...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-018-0085-7
更新日期:2019-01-01 00:00:00
abstract::We describe the use of a microfabricated cell culture substrate, consisting of a uniform array of closely spaced, vertical, elastomeric microposts, to study the effects of substrate rigidity on cell function. Elastomeric micropost substrates are micromolded from silicon masters comprised of microposts of different hei...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2010.189
更新日期:2011-02-01 00:00:00
abstract::The genomic instability of stem cells in culture, caused by their routine in vitro propagation or by their genetic manipulation, is deleterious both for their clinical application and for their use in basic research. Frequent evaluation of the genomic integrity of stem cells is thus required, and it is usually perform...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.051
更新日期:2013-05-01 00:00:00
abstract::Social recognition (SR) enables rodents to distinguish between familiar and novel conspecifics, largely through individual odor cues. SR tasks utilize the tendency for a male to sniff and interact with a novel individual more than a familiar individual. Many paradigms have been used to study the roles of the neuropept...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2009.141
更新日期:2009-01-01 00:00:00
abstract::RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially expressed genes across different conditions (e.g., tissues, perturbations) while opt...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.099
更新日期:2013-09-01 00:00:00
abstract::This protocol describes the principles and methods used for the preparation of cryopreserved cell stocks. Following these procedures will ensure the availability of reproducible cultures for use within a single laboratory at different times and for different collaborating laboratories. Although the basic principle is ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2008.190
更新日期:2008-01-01 00:00:00
abstract::This protocol describes the synthesis of oligo(poly(ethylene glycol) fumarate) (OPF; 1-35 kDa; a polymer useful for tissue engineering applications) by a one-pot reaction of poly(ethylene glycol) (PEG) and fumaryl chloride. The procedure involves three parts: dichloromethane and PEG are first dried; the reaction step ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.055
更新日期:2012-05-31 00:00:00
abstract::Apoptosis is a critical factor in AIDS and other viral illnesses, cerebral and myocardial ischemia, autoimmune and neurodegenerative states, organ and bone marrow transplant rejection, and tumor response to chemotherapy and radiation. Improved methods to identify sites of apoptosis are increasing our understanding of ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.17
更新日期:2006-01-01 00:00:00
abstract::High-throughput sequencing of the variable domains of immune receptors (antibodies and T cell receptors (TCRs)) is of key importance in the understanding of adaptive immune responses in health and disease. However, the sequencing of both immune receptor chains (VH+VL or TCRβ/δ+TCRα/γ) at the single-cell level for typi...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2016.024
更新日期:2016-03-01 00:00:00
abstract::This protocol describes a simple but robust microfluidic assay combining three-dimensional (3D) and two-dimensional (2D) cell culture. The microfluidic platform comprises hydrogel-incorporating chambers between surface-accessible microchannels. By using this platform, well-defined biochemical and biophysical stimuli c...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.051
更新日期:2012-06-07 00:00:00
abstract::Mass spectrometry (MS)-based proteomics has become the preferred tool for the analysis of protein phosphorylation. To be successful at such an endeavor, there is a requirement for an efficient enrichment of phosphopeptides. This is necessary because of the substoichiometric nature of phosphorylation at a given site an...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.010
更新日期:2013-03-01 00:00:00
abstract::During biosynthesis on the ribosome, an elongating nascent polypeptide chain can begin to fold, in a process that is central to all living systems. Detailed structural studies of co-translational protein folding are now beginning to emerge; such studies were previously limited, at least in part, by the inherently dyna...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2016.101
更新日期:2016-08-01 00:00:00
abstract::One of the challenges for modern neuroscience is to understand the rules of concerted neuronal function in vivo. This question can be addressed using noninvasive high-resolution imaging techniques like two-photon microscopy. This protocol describes a versatile approach for in vivo two-photon calcium imaging of neural ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.58
更新日期:2006-01-01 00:00:00
abstract::The study of angiogenic endothelial cells (ECs) has in recent years greatly stimulated multiple fields of vascular biology research. A number of cellular models and numerous complex developmental, manipulatory and tumor animal models have been developed to study angiogenesis in vitro and in vivo. To connect the versat...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2009.96
更新日期:2009-01-01 00:00:00