Abstract：
:Interactions of proteins with DNA mediate many critical nuclear functions. Chromatin immunoprecipitation (ChIP) is a robust technique for studying protein-DNA interactions. Current ChIP assays, however, either require large cell numbers, which prevent their application to rare cell samples or small-tissue biopsies, or involve lengthy procedures. We describe here a 1-day micro ChIP (microChIP) protocol suitable for up to eight parallel histone and/or transcription factor immunoprecipitations from a single batch of 1,000 cells. MicroChIP technique is also suitable for monitoring the association of one protein with multiple genomic sites in 100 cells. Alterations in cross-linking and chromatin preparation steps also make microChIP applicable to approximately 1-mm(3) fresh- or frozen-tissue biopsies. From cell fixation to PCR-ready DNA, the procedure takes approximately 8 h for 16 ChIPs.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Dahl JA,Collas Pdoi
10.1038/nprot.2008.68subject
Has Abstractpub_date
2008-01-01 00:00:00pages
1032-45issue
6eissn
1754-2189issn
1750-2799pii
nprot.2008.68journal_volume
3pub_type
杂志文章相关文献
Nature Protocols文献大全abstract：:An important goal of the analysis of sequenced genomes of microbial pathogens is to improve the therapy of infectious diseases. In this context, a major challenge is to detect genomic-level evolutionary changes that increase microbial virulence. TimeZone, a genome analysis software package, is designed to detect footp...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2013.031
更新日期：2013-04-01 00:00:00
abstract：:This protocol describes a method to obtain spatially resolved proteomic maps of specific compartments within living mammalian cells. An engineered peroxidase, APEX2, is genetically targeted to a cellular region of interest. Upon the addition of hydrogen peroxide for 1 min to cells preloaded with a biotin-phenol substr...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2016.018
更新日期：2016-03-01 00:00:00
abstract：:Improvement of cellular uptake and cellular localization is still one of the main obstacles to the development of antisense-antigene therapeutics, including peptide nucleic acid (PNA). Cell-penetrating peptides (CPPs) such as Tat peptide and polyarginine have been widely used to improve the cellular uptake of PNA and ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.92
更新日期：2006-01-01 00:00:00
abstract：:Gene tagging with fluorescent proteins is essential for investigations of the dynamic properties of cellular proteins. CRISPR-Cas9 technology is a powerful tool for inserting fluorescent markers into all alleles of the gene of interest (GOI) and allows functionality and physiological expression of the fusion protein. ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2018.042
更新日期：2018-06-01 00:00:00
abstract：:Several cell death assays have been developed based on a single biochemical parameter such as caspase activation or plasma membrane permeabilization. Our fluorescent apoptosis/necrosis (FAN) assay directly measures cell death and distinguishes between caspase-dependent apoptosis and caspase-independent necrosis of cel...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2016.085
更新日期：2016-08-01 00:00:00
abstract：:Here we describe a protocol to dissect the peroxisomal matrix protein import pathway using a cell-free in vitro system. The system relies on a postnuclear supernatant (PNS), which is prepared from rat/mouse liver, to act as a source of peroxisomes and cytosolic components. A typical in vitro assay comprises the follow...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2016.147
更新日期：2016-12-01 00:00:00
abstract：:The goal of many current studies of neovascularization is to define the phenotype of vascular cell populations of different origins and to determine how such cells promote assembly of vascular channel. Here, we describe a protocol to immunophenotype vascular cells by high-resolution imaging and by fluorescence-activat...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.537
更新日期：2008-01-01 00:00:00
abstract：:Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers thr...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2010.197
更新日期：2011-03-01 00:00:00
abstract：:Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS2) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-019-0131-0
更新日期：2019-04-01 00:00:00
abstract：:In this report we describe the development of a standardized three-dimensional (3D) system of the human oral mucosa based on an immortalized human oral keratinocyte cell line (OKF6/TERT-2). The procedure takes approximately 2-3 weeks to complete and includes three main stages: preparation of collagen-embedded fibrobla...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.323
更新日期：2006-01-01 00:00:00
abstract：:The pig has emerged as an important large animal model in biomedical and pharmaceutical research. We describe a protocol for high-efficiency germline transgenesis and sustained transgene expression in pigs by using the Sleeping Beauty (SB) transposon system. The protocol is based on co-injection of a plasmid encoding ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2014.010
更新日期：2014-04-01 00:00:00
abstract：:Herein we describe a protocol that uses hollow-fiber flow field-flow fractionation (FFF) coupled with multiangle light scattering (MALS) for hydrodynamic size-based separation and characterization of complex protein aggregates. The fractionation method, which requires 1.5 h to run, was successfully modified from the a...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2015.009
更新日期：2015-01-01 00:00:00
abstract：:The analysis of large microbiome data sets holds great promise for the delineation of the biological and metabolic functioning of living organisms and their role in the environment. In the midst of this genomic puzzle, viruses, especially those that infect microbial communities, represent a major reservoir of genetic ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2017.063
更新日期：2017-08-01 00:00:00
abstract：:Here, we describe a simple protocol for the design and construction of a laser-guided direct writing (LGDW) system able to micropattern the self-assembly of liver sinusoid-like structures with micrometer resolution in vitro. To the best of our knowledge, LGDW is the only technique able to pattern cells "on the fly" wi...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.386
更新日期：2006-01-01 00:00:00
abstract：:Multiplex-fluorescence in situ hybridization (M-FISH) was initially developed to stain human chromosomes--the 22 autosomes and X and Y sex chromosomes--with uniquely distinctive colors to facilitate karyotyping. The characteristic spectral signatures of all different combinations of fluorochromes are determined by mul...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.160
更新日期：2006-01-01 00:00:00
abstract：:The colorimetric bio-barcode assay is a red-to-blue color change-based protein detection method with ultrahigh sensitivity. This assay is based on both the bio-barcode amplification method that allows for detecting miniscule amount of targets with attomolar sensitivity and gold nanoparticle-based colorimetric DNA dete...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.201
更新日期：2007-01-01 00:00:00
abstract：:This protocol describes a method for converting short single-stranded and double-stranded DNA into libraries compatible with high-throughput sequencing using Illumina technology. This method has primarily been developed to improve sequence retrieval from ancient DNA, but it is also applicable to the sequencing of shor...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2013.038
更新日期：2013-04-01 00:00:00
abstract：:We describe the implementation and use of an adaptive imaging framework for optimizing spatial resolution and signal strength in a light-sheet microscope. The framework, termed AutoPilot, comprises hardware and software modules for automatically measuring and compensating for mismatches between light-sheet and detecti...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-018-0043-4
更新日期：2018-11-01 00:00:00
abstract：:In this protocol, we describe cryoimmunolabeling methods for the subcellular localization of proteins and certain lipids. The methods start with chemical fixation of cells and tissue in formaldehyde (FA) and/or glutaraldehyde (GA), sometimes supplemented with acrolein. Cell and tissue blocks are then immersed in 2.3 M...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.365
更新日期：2007-01-01 00:00:00
abstract：:The glycocalyx comprises glycosylated proteins and lipids and fcorms the outermost layer of cells. It is involved in fundamental inter- and intracellular processes, including non-self-cell and self-cell recognition, cell signaling, cellular structure maintenance, and immune protection. Characterization of the glycocal...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-020-0350-4
更新日期：2020-08-01 00:00:00
abstract：:Periodontal disease (PD) is a common dental disease associated with the interaction between dysbiotic oral microbiota and host immunity. It is a prevalent disease, resulting in loss of gingival tissue, periodontal ligament, cementum and alveolar bone. PD is a major form of tooth loss in the adult population. Experimen...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-018-0035-4
更新日期：2018-10-01 00:00:00
abstract：:Fluorescent microspheres are commonly used to assess bone blood supply in large animals, but the technique is not widely used in smaller mammals, as traditional methods such as reference blood sampling, ventilation and catheterization are not easily applied. This protocol describes a viable alternative for measuring b...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2009.190
更新日期：2009-01-01 00:00:00
abstract：:This protocol describes a method for directing the expression of genes of interest into postmitotic neocortical neurons in vivo. Microinjection of a DNA plasmid-amphiphilic molecule mix into the neocortex followed by delivery of an ad hoc electric pulse protocol during the first few days of life in mice allows rapid, ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2015.001
更新日期：2015-01-01 00:00:00
abstract：:The tracking of cell fate, shape and migration is an essential component in the study of the development of multicellular organisms. Here we report a protocol that uses the protein Kaede, which is fluorescent green after synthesis but can be photoconverted red by violet or UV light. We have used Kaede along with confo...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.96
更新日期：2006-01-01 00:00:00
abstract：:This protocol describes pulsed-field gel electrophoresis (PFGE), a method developed for separation of large DNA molecules. Whereas standard DNA gel electrophoresis commonly resolves fragments up to approximately 50 kb in size, PFGE fractionates DNA molecules up to 10 Mb. The mechanism driving these separations exploit...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.94
更新日期：2007-01-01 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：:This protocol describes a cell-free system for studying vertebrate centromere and kinetochore formation. We reconstitute tandem arrays of centromere protein A (CENP-A) nucleosomes as a substrate for centromere and kinetochore assembly. These chromatin substrates are immobilized on magnetic beads and then incubated in ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2012.112
更新日期：2012-10-01 00:00:00
abstract：:Desorption electrospray ionization (DESI) allows the direct analysis of ordinary objects or pre-processed samples under ambient conditions. Among other applications, DESI is used to identify and record spatial distributions of lipids and drug molecules in biological tissue sections. This technique does not require sam...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2008.11
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：:The adeno-associated virus (AAV) is one of the most promising viral vectors for human gene therapy. As with any potential therapeutic system, a thorough understanding of it at the in vitro and in vivo levels is required. Over the years, numerous methods have been developed to better characterize AAV vectors. These met...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.207
更新日期：2006-01-01 00:00:00
