Production of a site- and phosphorylation state-specific antibody.

abstract：:The direct detection of drug-protein interactions in living cells is a major challenge in drug discovery research. Recently, we introduced an approach termed thermal proteome profiling (TPP), which enables the monitoring of changes in protein thermal stability across the proteome using quantitative mass spectrometry. ...

journal_title：Nature protocols

authors： Franken H,Mathieson T,Childs D,Sweetman GM,Werner T,Tögel I,Doce C,Gade S,Bantscheff M,Drewes G,Reinhard FB,Huber W,Savitski MM

更新日期：2015-10-01 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

authors： Vermeeren P,van der Lubbe SCC,Fonseca Guerra C,Bickelhaupt FM,Hamlin TA

更新日期：2020-02-01 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：: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 d...

journal_title：Nature protocols

authors： Nelson JD,Denisenko O,Bomsztyk K

更新日期：2006-01-01 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：: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

authors： Graf M,Lihter M,Thakur M,Georgiou V,Topolancik J,Ilic BR,Liu K,Feng J,Astier Y,Radenovic A

更新日期：2019-04-01 00:00:00

abstract：:Glycoproteins are involved in diverse biological processes ranging from extracellular contact and recognition to intracellular signaling. Crystal structures of glycoproteins would yield tremendous insight into these processes. But glycoprotein structural analysis has been hindered by difficulties in expressing milligr...

journal_title：Nature protocols

authors： Lee JE,Fusco ML,Saphire EO

更新日期：2009-01-01 00:00:00

abstract：:Brachypodium distachyon is emerging as a new model system for bridging research into temperate cereal crops, such as wheat and barley, and for promoting research in novel biomass grasses. Here, we provide an adapter ligation PCR protocol that allows the large-scale characterization of T-DNA insertions into the genome ...

journal_title：Nature protocols

authors： Thole V,Alves SC,Worland B,Bevan MW,Vain P

更新日期：2009-01-01 00:00:00

abstract：:Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions ...

journal_title：Nature protocols

authors： Jeffries CM,Graewert MA,Blanchet CE,Langley DB,Whitten AE,Svergun DI

更新日期：2016-11-01 00:00:00

abstract：:Rapid evaluation of microbial cell-surface carbohydrates is essential to understanding the mechanisms by which bacteria use glycans to establish pathogenic or symbiotic relationships. Microbial glycan analysis is complicated both by the vast diversity of possible carbohydrate structures and by their dynamic nature. Ba...

journal_title：Nature protocols

authors： Hsu KL,Mahal LK

更新日期：2006-01-01 00:00:00

abstract：:Laser-mediated gene transfection into mammalian cells has recently emerged as a powerful alternative to more traditional transfection techniques. In particular, the use of a femtosecond-pulsed laser operating in the near-infrared (NIR) region has been proven to provide single-cell selectivity, localized delivery, low ...

journal_title：Nature protocols

authors： Antkowiak M,Torres-Mapa ML,Stevenson DJ,Dholakia K,Gunn-Moore FJ

更新日期：2013-06-01 00:00:00

abstract：:This protocol describes a method combining phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers to characterize the germination of single bacterial spores. The characterization consists of the following steps: (i) loading heat-activated dormant spores into a temperature-controlled micros...

journal_title：Nature protocols

authors： Kong L,Zhang P,Wang G,Yu J,Setlow P,Li YQ

更新日期：2011-05-01 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

authors： Stacey GN,Masters JR

更新日期：2008-01-01 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：:Cell proliferation may be measured in vivo by quantifying DNA synthesis with isotopically labeled deoxyribonucleotide precursors. Deuterium-labeled glucose is one such precursor which, because it achieves high levels of enrichment for a short period, is well suited to the study of rapidly dividing cells, in contrast t...

journal_title：Nature protocols

authors： Macallan DC,Asquith B,Zhang Y,de Lara C,Ghattas H,Defoiche J,Beverley PC

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

authors： Anders S,McCarthy DJ,Chen Y,Okoniewski M,Smyth GK,Huber W,Robinson MD

更新日期：2013-09-01 00:00:00

abstract：:In the past decade, Drosophila has emerged as an ideal model organism for studying the genetic components of sleep as well as its regulation and functions. In fruit flies, sleep can be conveniently estimated by measuring the locomotor activity of the flies using techniques and instruments adapted from the field of cir...

journal_title：Nature protocols

authors： Gilestro GF

更新日期：2012-04-26 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：:The development of single-molecule switching (SMS) fluorescence microscopy (also called single-molecule localization microscopy) over the last decade has enabled researchers to image cell biological structures at unprecedented resolution. Using two opposing objectives in a so-called 4Pi geometry doubles the available ...

journal_title：Nature protocols

authors： Wang J,Allgeyer ES,Sirinakis G,Zhang Y,Hu K,Lessard MD,Li Y,Diekmann R,Phillips MA,Dobbie IM,Ries J,Booth MJ,Bewersdorf J

更新日期：2020-12-16 00:00:00

abstract：:The terminal monosaccharide of cell surface glycoconjugates is typically a sialic acid (SA), and aberrant sialylation is involved in several diseases. Several methodological approaches in sample preparation and subsequent analysis using mass spectrometry (MS) have enabled the identification of glycosylation sites and ...

journal_title：Nature protocols

authors： Palmisano G,Lendal SE,Engholm-Keller K,Leth-Larsen R,Parker BL,Larsen MR

更新日期：2010-12-01 00:00:00

abstract：:The analysis of highly hydrophobic proteins is still an analytical challenge. Using a recombinant gamma-aminobutyric acid A (GABAA)-receptor subunit as a model protein, we developed a gel-based proteomic approach for high MS/MS-peptide sequence coverage identification. Protein samples were separated by multi-dimension...

journal_title：Nature protocols

authors： Kang SU,Fuchs K,Sieghart W,Pollak A,Csaszar E,Lubec G

更新日期：2009-01-01 00:00:00

abstract：:Adult stem cell-based organoid technology is a versatile tool for the generation and long-term maintenance of near-native 3D epithelial tissues in vitro. The generation of cancer organoids from primary patient material enables a range of therapeutic agents to be tested in the resulting organoid cultures. Patient-deriv...

journal_title：Nature protocols

authors： Driehuis E,Kretzschmar K,Clevers H

更新日期：2020-10-01 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

authors： Herschleb J,Ananiev G,Schwartz DC

更新日期：2007-01-01 00:00:00

abstract：:Biominerals serve as critical structures of living systems and play important roles in biochemical processes. Understanding their crystallization mechanisms is therefore central to many areas of biology, biogeoscience, and biochemistry. Some biominerals, such as bone and dentin, are hierarchical nanocomposite structur...

journal_title：Nature protocols

authors： Zhang X,He Y,Liu J,Bowden ME,Kovarik L,Mao SX,Wang C,De Yoreo JJ,Rosso KM

更新日期：2018-09-01 00:00:00

abstract：:We describe a protocol for the insertion of ultrashort single-walled carbon nanotubes (SWCNTs) to form nanopores in a Montal-Mueller lipid bilayer. The SWCNTs are designed to bind to a specific analyte of interest; binding will result in the reduction of current in single-channel recording experiments. The first stage...

journal_title：Nature protocols

authors： Liu L,Xie J,Li T,Wu HC

更新日期：2015-11-01 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

authors： Guse A,Fuller CJ,Straight AF

更新日期：2012-10-01 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

authors： Shiraishi T,Nielsen PE

更新日期：2006-01-01 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

authors： Lickwar CR,Mueller F,Lieb JD

更新日期：2013-01-01 00:00:00

abstract：:Gram-negative and Gram-positive bacteria release a variety of membrane vesicles through different formation routes. Knowledge of the structure, molecular cargo and function of bacterial extracellular vesicles (BEVs) is primarily obtained from bacteria cultured in laboratory conditions. BEVs in human body fluids have b...

journal_title：Nature protocols

authors： Tulkens J,De Wever O,Hendrix A

更新日期：2020-01-01 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

authors： Pratt JM,Simpson DM,Doherty MK,Rivers J,Gaskell SJ,Beynon RJ

更新日期：2006-01-01 00:00:00