Characterizing peptides in individual mammalian cells using mass spectrometry.

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

authors： Laib AM,Bartol A,Alajati A,Korff T,Weber H,Augustin HG

更新日期：2009-01-01 00:00:00

abstract：:We describe a step-by-step protocol for measuring the stable products of the nitric oxide (NO) pathway: nitrite, nitrite plus nitrate and nitrate. This described protocol is easy to apply and is about 50 times more sensitive than the commonly used Griess reaction or commercially available assay kits based on the Gries...

journal_title：Nature protocols

authors： Nussler AK,Glanemann M,Schirmeier A,Liu L,Nüssler NC

更新日期：2006-01-01 00:00:00

abstract：:Mass spectrometry-based phosphoproteomic analysis is a powerful method for gaining a global, unbiased understanding of cellular signaling. Its accuracy and comprehensiveness stands or falls with the quality and choice of the applied phosphopeptide prefractionation strategy. This protocol covers a powerful but simple a...

journal_title：Nature protocols

authors： Zarei M,Sprenger A,Rackiewicz M,Dengjel J

更新日期：2016-01-01 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

authors： McDaniel JR,DeKosky BJ,Tanno H,Ellington AD,Georgiou G

更新日期：2016-03-01 00:00:00

abstract：:High-throughput transcriptional analysis has unveiled a myriad of novel RNAs. However, technical constraints in RNA sequencing library preparation and platform performance hamper the identification of rare transcripts contained within the RNA repertoire. Herein we present targeted-RNA directional sequencing (TARDIS), ...

journal_title：Nature protocols

authors： Portal MM,Pavet V,Erb C,Gronemeyer H

更新日期：2015-12-01 00:00:00

abstract：:Association studies can focus on candidate gene(s), a particular genomic region, or adopt a genome-wide association approach, each of which has implications for marker selection. The strategy for marker selection will affect the statistical power of the study to detect a disease association and is a crucial element of...

journal_title：Nature protocols

authors： Pettersson FH,Anderson CA,Clarke GM,Barrett JC,Cardon LR,Morris AP,Zondervan KT

更新日期：2009-01-01 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：: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

authors： Jones RC,Capen DE,Cohen KS,Munn LL,Jain RK,Duda DG

更新日期：2008-01-01 00:00:00

abstract：:Human embryonic stem (hES) cells are self-renewing, pluripotent cells that are valuable research tools and hold promise for use in regenerative medicine. Most hES cell lines are derived from cryopreserved human embryos that were created during in vitro fertilization (IVF) and are in excess of clinical need. Embryos th...

journal_title：Nature protocols

authors： Lerou PH,Yabuuchi A,Huo H,Miller JD,Boyer LF,Schlaeger TM,Daley GQ

更新日期：2008-01-01 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

authors： Gansauge MT,Meyer M

更新日期：2013-04-01 00:00:00

abstract：:Recombineering is an efficient method of in vivo genetic engineering applicable to chromosomal as well as episomal replicons in Escherichia coli. This method circumvents the need for most standard in vitro cloning techniques. Recombineering allows construction of DNA molecules with precise junctions without constraint...

journal_title：Nature protocols

authors： Sharan SK,Thomason LC,Kuznetsov SG,Court DL

更新日期：2009-01-01 00:00:00

abstract：:Systematic complex genetic interaction studies have provided insight into high-order functional redundancies and genetic network wiring of the cell. Here, we describe a method for screening and quantifying trigenic interactions from ordered arrays of yeast strains grown on agar plates as individual colonies. The proto...

journal_title：Nature protocols

authors： Kuzmin E,Rahman M,VanderSluis B,Costanzo M,Myers CL,Andrews BJ,Boone C

更新日期：2021-01-18 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

authors： Shiraishi T,Nielsen PE

更新日期：2006-01-01 00:00:00

abstract：:Live single-cell mass spectrometry (live MS) provides a mass spectrum that shows thousands of metabolite peaks from a single live plant cell within minutes. By using an optical microscope, a cell is chosen for analysis and a metal-coated nanospray microcapillary tip is used to remove the cell's contents. After adding ...

journal_title：Nature protocols

authors： Fujii T,Matsuda S,Tejedor ML,Esaki T,Sakane I,Mizuno H,Tsuyama N,Masujima T

更新日期：2015-09-01 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

authors： Kinard LA,Kasper FK,Mikos AG

更新日期：2012-05-31 00:00:00

abstract：:Establishing a small animal model that accurately recapitulates hepatotropic pathogens, including hepatitis C virus (HCV) infection and immunopathogenesis, is essential for the study of hepatitis virus-induced liver disease and for therapeutics development. This protocol describes our recently developed humanized mous...

journal_title：Nature protocols

authors： Bility MT,Zhang L,Washburn ML,Curtis TA,Kovalev GI,Su L

更新日期：2012-09-01 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

authors： Serrat MA

更新日期：2009-01-01 00:00:00

abstract：:More than 400,000 people each year suffer adverse effects following bites from venomous snakes. However, snake venom is also a rich source of bioactive molecules with known or potential therapeutic applications. Manually 'milking' snakes is the most common method to obtain venom. Safer alternative methods to produce v...

journal_title：Nature protocols

authors： Puschhof J,Post Y,Beumer J,Kerkkamp HM,Bittenbinder M,Vonk FJ,Casewell NR,Richardson MK,Clevers H

更新日期：2021-01-27 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

authors： Nolbrant S,Heuer A,Parmar M,Kirkeby A

更新日期：2017-09-01 00:00:00

abstract：:In order to meaningfully analyze common and rare genetic variants, results from genome-wide association studies (GWASs) of multiple cohorts need to be combined in a meta-analysis in order to obtain enough power. This requires all cohorts to have the same single-nucleotide polymorphisms (SNPs) in their GWASs. To this e...

journal_title：Nature protocols

authors： van Leeuwen EM,Kanterakis A,Deelen P,Kattenberg MV,Genome of the Netherlands Consortium.,Slagboom PE,de Bakker PI,Wijmenga C,Swertz MA,Boomsma DI,van Duijn CM,Karssen LC,Hottenga JJ

更新日期：2015-09-01 00:00:00

abstract：:This protocol describes the efficient, generally applicable Ullmann coupling reaction of bromaminic acid with alkyl- or aryl-amines in phosphate buffer under microwave irradiation using elemental copper as a catalyst. The reaction leads to a number of biologically active compounds. As a prototypical example, the synth...

journal_title：Nature protocols

authors： Baqi Y,Müller CE

更新日期：2010-05-01 00:00:00

abstract：:Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and p...

journal_title：Nature protocols

authors： Butler HJ,Ashton L,Bird B,Cinque G,Curtis K,Dorney J,Esmonde-White K,Fullwood NJ,Gardner B,Martin-Hirsch PL,Walsh MJ,McAinsh MR,Stone N,Martin FL

更新日期：2016-04-01 00:00:00

abstract：:This protocol details a subset of assays developed within the touchscreen platform to measure various aspects of executive function in rodents. Three main procedures are included: extinction, measuring the rate and extent of curtailing a response that was previously, but is no longer, associated with reward; reversal ...

journal_title：Nature protocols

authors： Mar AC,Horner AE,Nilsson SR,Alsiö J,Kent BA,Kim CH,Holmes A,Saksida LM,Bussey TJ

更新日期：2013-10-01 00:00:00

abstract：:A procedure for the synthesis of N-succinimidyl 3-iodobenzoate labeled with any iodine isotope ([*I]SIB), which is an agent used in the radioiodination of proteins and peptides, from its tin precursor N-succinimidyl 3-(tri-n-butylstannyl)benzoate (STB) is described. Also included are protocols for the synthesis of an ...

journal_title：Nature protocols

authors： Vaidyanathan G,Zalutsky MR

更新日期：2006-01-01 00:00:00

abstract：:Forebrain γ-aminobutyric acid (GABA) interneurons have crucial roles in high-order brain function via modulating network activities and plasticity, and they are implicated in many psychiatric disorders. Availability of enriched functional human forebrain GABA interneurons, especially those from people affected by GABA...

journal_title：Nature protocols

authors： Liu Y,Liu H,Sauvey C,Yao L,Zarnowska ED,Zhang SC

更新日期：2013-09-01 00:00:00

abstract：:This protocol outlines steps for optimizing the transfection of adherent primary mammalian cells using the readily available off-the-shelf cationic polymer, 25-kDa branched polyethylenimine (bPEI25). Transfection efficiency of cationic polymers varies among cell lines and is highly dependent on the conditions and envi...

journal_title：Nature protocols

authors： Hsu CY,Uludağ H

更新日期：2012-04-19 00:00:00

abstract：:Apoptosis plays a pivotal role in the regulation of cell turnover, and a defect or an excess of apoptosis has been implicated in several human diseases. Apoptosis is activated from an extracellular death signal, or from an internal pathway starting from the endoplasmatic reticulum or the mitochondria. To investigate t...

journal_title：Nature protocols

authors： Ferlini C,Scambia G

更新日期：2007-01-01 00:00:00

abstract：:Determining enantiomeric excess (e.e.) in chiral compounds is key to development of chiral catalyst auxiliaries and chiral drugs. Here we describe a sensitive and robust fluorescence-based assay for determining e.e. in mixtures of enantiomers of 1,2- and 1,3-diols, chiral amines, amino alcohols, and amino-acid esters....

journal_title：Nature protocols

authors： Shcherbakova EG,James TD,Anzenbacher P Jr

更新日期：2020-07-01 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

authors： Hiei Y,Komari T

更新日期：2008-01-01 00:00:00

abstract：:Targeted nucleases, including zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9), have provided researchers with the ability to manipulate nearly any genomic sequence in hu...

journal_title：Nature protocols

authors： Liu J,Gaj T,Yang Y,Wang N,Shui S,Kim S,Kanchiswamy CN,Kim JS,Barbas CF 3rd

更新日期：2015-11-01 00:00:00