A protocol for phenotypic detection and enumeration of circulating endothelial cells and circulating progenitor cells in human blood.

abstract：:This protocol describes a simple silver staining method used to visualize DNA fragments and other organic molecules with unsurpassed detail following traditional polyacrylamide gel electrophoresis (PAGE). Sensitivity rivals radioisotopic methods and DNA in the picogram range can be reliably detected. The described pro...

journal_title：Nature protocols

authors： Bassam BJ,Gresshoff PM

更新日期：2007-01-01 00:00:00

abstract：:Post-translational modifications alter protein structure, affecting activity, stability, localization and/or binding partners. Antibodies that specifically recognize post-translationally modified proteins have a number of uses including immunocytochemistry and immunoprecipitation of the modified protein to purify prot...

journal_title：Nature protocols

authors： Arur S,Schedl T

更新日期：2014-02-01 00:00:00

abstract：:The CRISPR-Cas9 genome-editing tool and the availability of whole-genome sequences from plant species have revolutionized our ability to introduce targeted mutations into important crop plants, both to explore genetic changes and to introduce new functionalities. Here, we describe protocols adapting the CRISPR-Cas9 sy...

journal_title：Nature protocols

authors： Osakabe Y,Liang Z,Ren C,Nishitani C,Osakabe K,Wada M,Komori S,Malnoy M,Velasco R,Poli M,Jung MH,Koo OJ,Viola R,Nagamangala Kanchiswamy C

更新日期：2018-12-01 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

authors： Royer LA,Lemon WC,Chhetri RK,Keller PJ

更新日期：2018-11-01 00:00:00

abstract：:The effect of genetic mutation on phenotype is of significant interest in genetics. The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP). An nsSNP could potentially affect the function of the protein, sub...

journal_title：Nature protocols

authors： Kumar P,Henikoff S,Ng PC

更新日期：2009-01-01 00:00:00

abstract：:Traumatic brain injury (TBI) is a major cause of mortality and morbidity. Various attempts have been made to replicate clinical TBI using animal models. The fluid-percussion model (FP) is one of the oldest and most commonly used models of experimentally induced TBI. Both central (CFP) and lateral (LFP) variations of t...

journal_title：Nature protocols

authors： Kabadi SV,Hilton GD,Stoica BA,Zapple DN,Faden AI

更新日期：2010-09-01 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

authors： Benaglia S,Gisbert VG,Perrino AP,Amo CA,Garcia R

更新日期：2018-12-01 00:00:00

abstract：:In this report, we describe a two-step protocol for labeling of an affinity-purified antibody to biotin with horseradish peroxidase (HRP) using cyanuric chloride (CC) as a bridge. The enzyme was first modified with CC, and following chromatography on a PD-10 column, the activated HRP was incubated with the antibody to...

journal_title：Nature protocols

authors： Abuknesha RA,Jeganathan F,Wu J,Baalawy Z

更新日期：2009-01-01 00:00:00

abstract：:The ability to isolate and analyze rare circulating tumor cells (CTCs) has the potential to further our understanding of cancer metastasis and enhance the care of cancer patients. In this protocol, we describe the procedure for isolating rare CTCs from blood samples by using tumor antigen-independent microfluidic CTC-...

journal_title：Nature protocols

authors： Karabacak NM,Spuhler PS,Fachin F,Lim EJ,Pai V,Ozkumur E,Martel JM,Kojic N,Smith K,Chen PI,Yang J,Hwang H,Morgan B,Trautwein J,Barber TA,Stott SL,Maheswaran S,Kapur R,Haber DA,Toner M

更新日期：2014-03-01 00:00:00

abstract：:This protocol describes a method for direct labeling and detection of small RNAs present in total RNA by splinted ligation. The assay uses a small RNA-specific bridge oligonucleotide to form base pairs with the small RNA and a 5'-end-radiolabeled ligation oligonucleotide. The captured small RNA is directly labeled by ...

journal_title：Nature protocols

authors： Maroney PA,Chamnongpol S,Souret F,Nilsen TW

更新日期：2008-01-01 00:00:00

abstract：:The transmembrane (TM) anchors of cell surface proteins have been one of the 'blind spots' in structural biology because they are generally very hydrophobic, sometimes dynamic, and thus difficult targets for structural characterization. A plethora of examples show these membrane anchors are not merely anchors but can ...

journal_title：Nature protocols

authors： Fu Q,Piai A,Chen W,Xia K,Chou JJ

更新日期：2019-08-01 00:00:00

abstract：:This protocol describes procedures for performing fluorescence resonance energy transfer (FRET) microscopy analysis by three different methods: acceptor photobleaching, sensitized emission and spectral imaging. We also discuss anisotropy and fluorescence lifetime imaging microscopy-based FRET techniques. By using the ...

journal_title：Nature protocols

authors： Broussard JA,Rappaz B,Webb DJ,Brown CM

更新日期：2013-02-01 00:00:00

abstract：:Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long read...

journal_title：Nature protocols

authors： Yue JX,Liti G

更新日期：2018-06-01 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

authors： Yu X,LaBaer J

更新日期：2015-05-01 00:00:00

abstract：:Large-insert BAC (bacterial artificial chromosome) and BIBAC (binary BAC) libraries are essential for modern genomics research for all organisms. We helped pioneer the BAC and BIBAC technologies, and by using them we have constructed hundreds of BAC and BIBAC libraries for different species of plants, animals, marine ...

journal_title：Nature protocols

authors： Zhang HB,Scheuring CF,Zhang M,Zhang Y,Wu CC,Dong JJ,Li Y

更新日期：2012-02-16 00:00:00

abstract：:The partial reduction of electron-deficient pyrroles using either Birch (Li/NH(3)) or ammonia-free (Li/di-tert-butyl biphenyl) conditions allows formation of pyrroline compounds in good yield and, when combined with a reductive alkylation or similar approach, leads to highly functionalized, synthetically useful compou...

journal_title：Nature protocols

authors： Donohoe TJ,Thomas RE

更新日期：2007-01-01 00:00:00

abstract：:In most organisms, one crossover (CO) event inhibits the chances of another nearby event. The term used to describe this phenomenon is 'CO interference'. Here, we describe a protocol for quickly generating large data sets that are amenable to CO interference analysis in the flowering plant, Arabidopsis thaliana. We em...

journal_title：Nature protocols

authors： Berchowitz LE,Copenhaver GP

更新日期：2008-01-01 00:00:00

abstract：:In situ mRNA hybridization is one of the most powerful techniques for analyzing patterns of gene expression. However, its usefulness is limited in complex plant tissues by the need to fix, embed and section samples before localizing the desired mRNA. Here we present a robust whole-mount in situ hybridization method th...

journal_title：Nature protocols

authors： Rozier F,Mirabet V,Vernoux T,Das P

更新日期：2014-10-01 00:00:00

abstract：:ErmineJ is software for the analysis of functionally interesting patterns in large gene lists drawn from gene expression profiling data or other high-throughput genomics studies. It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. It allo...

journal_title：Nature protocols

authors： Gillis J,Mistry M,Pavlidis P

更新日期：2010-06-01 00:00:00

abstract：:Venous access catheters used in clinics are prone to biofilm contamination, contributing to chronic and nosocomial infections. Although several animal models for studying device-associated biofilms were previously described, only a few detailed protocols are currently available. Here we provide a protocol using totall...

journal_title：Nature protocols

authors： Chauhan A,Ghigo JM,Beloin C

更新日期：2016-03-01 00:00:00

abstract：:Analysis of the sequence and nature of protein N termini has many applications. Defining the termini of proteins for proteome annotation in the Human Proteome Project is of increasing importance. Terminomics analysis of protease cleavage sites in degradomics for substrate discovery is a key new application. Here we de...

journal_title：Nature protocols

authors： Kleifeld O,Doucet A,Prudova A,auf dem Keller U,Gioia M,Kizhakkedathu JN,Overall CM

更新日期：2011-09-22 00:00:00

abstract：:Although differences in protein staining intensity can often be visualized by difference gel electrophoresis, abundant proteins can obscure less abundant proteins, and quantification of post-translational modifications is difficult. We present a protocol for quantifying changes in the abundance of a specific protein o...

journal_title：Nature protocols

authors： Asara JM,Zhang X,Zheng B,Maroney LA,Christofk HR,Wu N,Cantley LC

更新日期：2006-01-01 00:00:00

abstract：:Hydroxyl radical footprinting has been widely used for studying the structure of DNA and DNA-protein complexes. The high reactivity and lack of base specificity of the hydroxyl radical makes it an excellent probe for high-resolution footprinting of DNA-protein complexes; this technique can provide structural detail th...

journal_title：Nature protocols

authors： Jain SS,Tullius TD

更新日期：2008-01-01 00:00:00

abstract：:Raman and Fourier transform IR (FTIR) microspectroscopic images of biological material (tissue sections) contain detailed information about their chemical composition. The challenge lies in identifying changes in chemical composition, as well as locating and assigning these changes to different conditions (pathology, ...

journal_title：Nature protocols

authors： Felten J,Hall H,Jaumot J,Tauler R,de Juan A,Gorzsás A

更新日期：2015-02-01 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

authors： Dongari-Bagtzoglou A,Kashleva H

更新日期：2006-01-01 00:00:00

abstract：:This protocol outlines the carboxyfluorescein diacetate succinimidyl ester (CFSE) method for following the proliferation of human lymphocytes in vitro and mouse lymphocytes both in vitro and in vivo. The method relies on the ability of CFSE to covalently label long-lived intracellular molecules with the highly fluores...

journal_title：Nature protocols

authors： Quah BJ,Warren HS,Parish CR

更新日期：2007-01-01 00:00:00

abstract：:Detailed biochemical analysis of unmanipulated germinal center (GC) B cells has not been achieved. Previously, we designed and used a simple, economical and new magnetic bead separation scheme for the purification of 'untouched' mature GC and non-GC B cells from the spleens of immunized mice and reported the first bio...

journal_title：Nature protocols

authors： Cato MH,Yau IW,Rickert RC

更新日期：2011-06-09 00:00:00

abstract：:We recently invented a method to produce highly potent siRNAs in Escherichia coli, based on the serendipitous discovery that ectopic expression of p19, a plant viral siRNA-binding protein, stabilizes otherwise unstable bacterial siRNAs, which we named pro-siRNAs for prokaryotic siRNAs. We present a detailed protocol d...

journal_title：Nature protocols

authors： Huang L,Lieberman J

更新日期：2013-12-01 00:00:00

abstract：:The human stomach contains two primary domains: the corpus, which contains the fundic epithelium, and the antrum. Each of these domains has distinct cell types and functions, and therefore each presents with unique disease pathologies. Here, we detail two protocols to differentiate human pluripotent stem cells (hPSCs)...

journal_title：Nature protocols

authors： Broda TR,McCracken KW,Wells JM

更新日期：2019-01-01 00:00:00

abstract：:Many techniques have been developed for studying inducible gene expression, but all of them are multicomponent systems consisting of cis-acting elements at the DNA or RNA level, trans-acting regulator proteins and/or small molecules as inducers. RNA thermometers are the only known single-component regulators of gene e...

journal_title：Nature protocols

authors： Neupert J,Bock R

更新日期：2009-01-01 00:00:00