Silver staining DNA in polyacrylamide gels.

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：: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：:With the advent of massively parallel sequencing, considerable work has gone into adapting chromosome conformation capture (3C) techniques to study chromosomal architecture at a genome-wide scale. We recently demonstrated that the inactive murine X chromosome adopts a bipartite structure using a novel 3C protocol, ter...

journal_title：Nature protocols

authors： Ramani V,Cusanovich DA,Hause RJ,Ma W,Qiu R,Deng X,Blau CA,Disteche CM,Noble WS,Shendure J,Duan Z

更新日期：2016-11-01 00:00:00

abstract：:Most currently available colorectal cancer (CRC) mouse models are not suitable for studying progression toward the metastatic stage. Recently, establishment of tumor organoid lines, either from murine CRC models or patients, and the possibility of engineering them with genome-editing technologies, have provided a larg...

journal_title：Nature protocols

authors： Fumagalli A,Suijkerbuijk SJE,Begthel H,Beerling E,Oost KC,Snippert HJ,van Rheenen J,Drost J

更新日期：2018-02-01 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：:Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions by structural matching) f...

journal_title：Nature protocols

authors： Tuncbag N,Gursoy A,Nussinov R,Keskin O

更新日期：2011-08-11 00:00:00

abstract：:RNA interference (RNAi) is an efficient method for silencing genes in cultured cells. Here we describe a simple RNAi approach for silencing genes in a cell type-specific and tissue-specific way in vivo. The approach, which mimics the means by which naturally occurring 'microRNA's are generated, uses a tissue-specific ...

journal_title：Nature protocols

authors： Rao MK,Wilkinson MF

更新日期：2006-01-01 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：: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

authors： Grootjans S,Hassannia B,Delrue I,Goossens V,Wiernicki B,Dondelinger Y,Bertrand MJ,Krysko DV,Vuylsteke M,Vandenabeele P,Vanden Berghe T

更新日期：2016-08-01 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：:The specialized microfold cells (M cells) in the follicle-associated epithelium (FAE) of intestinal Peyer's patches serve as antigen-sampling cells of the intestinal innate immune system. Unlike 'classical' enterocytes, they are able to translocate diverse particulates without digesting them. They act as pathways for ...

journal_title：Nature protocols

authors： Beloqui A,Brayden DJ,Artursson P,Préat V,des Rieux A

更新日期：2017-07-01 00:00:00

abstract：:Genetically encoded fluorescent proteins (FPs) are highly utilized in cell biology research to study proteins of interest or signal processes using biosensors. To perform well in specific applications, these FPs require a multitude of tailored properties. It is for this reason that they need to be optimized by using m...

journal_title：Nature protocols

authors： Bindels DS,Postma M,Haarbosch L,van Weeren L,Gadella TWJ Jr

更新日期：2020-02-01 00:00:00

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

authors： Lin YC,Li W,Chen H,Li Q,Sun YH,Shi R,Lin CY,Wang JP,Chen HC,Chuang L,Qu GZ,Sederoff RR,Chiang VL

更新日期：2014-09-01 00:00:00

abstract：:The world is on the cusp of a post-antibiotic era, but researchers and medical doctors have found a way forward-by looking back at how infections were treated before the advent of antibiotics, namely using phage therapy. Although bacteriophages (phages) continue to lack drug approval in Western medicine, an increasing...

journal_title：Nature protocols

authors： Luong T,Salabarria AC,Edwards RA,Roach DR

更新日期：2020-09-01 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：:This protocol is used to produce stably transformed tobacco (Nicotiana tabacum) NT1 cell lines, using Agrobacterium tumefaciens-mediated DNA delivery of a binary vector containing a gene encoding hepatitis B surface antigen and a gene encoding the kanamycin selection marker. The NT1 cultures, at the appropriate stage ...

journal_title：Nature protocols

authors： Mayo KJ,Gonzales BJ,Mason HS

更新日期：2006-01-01 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：:In cell affinity chromatography, type-specific cell separation is based on the interaction between cell-surface receptors and an immobilized ligand on a stationary matrix. This protocol describes the preparation of monolithic polyacrylamide and polydimethylacrylamide cryogel affinity matrices that can be used as a gen...

journal_title：Nature protocols

authors： Kumar A,Srivastava A

更新日期：2010-11-01 00:00:00

abstract：:Overexpression screens can be used to explore gene function in Drosophila melanogaster, but to demonstrate their full potential, comprehensive and systematic collections of fly strains are required. Here we provide a protocol for high-throughput cloning of Drosophila open-reading frames (ORFs) that are regulated by up...

journal_title：Nature protocols

authors： Bischof J,Sheils EM,Björklund M,Basler K

更新日期：2014-07-01 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：:Conventional gene expression studies analyze multiple cells simultaneously or single cells, for which the exact in vivo or in situ position is unknown. Although cellular heterogeneity can be discerned when analyzing single cells, any spatially defined attributes that underpin the heterogeneous nature of the cells cann...

journal_title：Nature protocols

authors： Chen J,Suo S,Tam PP,Han JJ,Peng G,Jing N

更新日期：2017-03-01 00:00:00

abstract：:The rodent malaria parasite Plasmodium chabaudi chabaudi shares many features with human malaria species, including P. falciparum, and is the in vivo model of choice for many aspects of malaria research in the mammalian host, from sequestration of parasitized erythrocytes, to antigenic variation and host immunity and ...

journal_title：Nature protocols

authors： Spence PJ,Cunningham D,Jarra W,Lawton J,Langhorne J,Thompson J

更新日期：2011-04-01 00:00:00

abstract：:The research community is in a race to understand the molecular mechanisms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, to repurpose currently available antiviral drugs and to develop new therapies and vaccines against coronavirus disease 2019 (COVID-19). One major challenge in achieving ...

journal_title：Nature protocols

authors： Gurumurthy CB,Quadros RM,Richardson GP,Poluektova LY,Mansour SL,Ohtsuka M

更新日期：2020-12-01 00:00:00

abstract：:We describe procedures for the synthesis of a fluorescent pyrimidine analog and its site-specific incorporation into a DNA oligomer. The 5'-protected and 3'-activated nucleoside 4 is synthesized in three steps with an overall yield of 40%. Site-specific incorporation into a DNA oligomer occurs with greater than 88% co...

journal_title：Nature protocols

authors： Greco NJ,Tor Y

更新日期：2007-01-01 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：: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：:Characterization of the cellular participants in tissue immune responses is crucial to understanding infection, cancer, autoimmunity, allergy, graft rejection and other immunological processes. Previous reports indicate that leukocytes in lung vasculature fail to be completely removed by perfusion. Several studies sug...

journal_title：Nature protocols

authors： Anderson KG,Mayer-Barber K,Sung H,Beura L,James BR,Taylor JJ,Qunaj L,Griffith TS,Vezys V,Barber DL,Masopust D

更新日期：2014-01-01 00:00:00

abstract：:The ability to rapidly generate large panels of antigen-specific human antibodies in a rodent would enable the efficient discovery of novel therapeutically useful antibodies. We have developed a system wherein human antigen-specific antibody-secreting plasmablasts can be enriched in vivo, in a severe combined immunode...

journal_title：Nature protocols

authors： Lin Z,Chiang NY,Chai N,Seshasayee D,Lee WP,Balazs M,Nakamura G,Swem LR

更新日期：2014-07-01 00:00:00

abstract：:The radial arm water maze (RAWM) contains six swim paths (arms) extending out of an open central area, with an escape platform located at the end of one arm (the goal arm). The goal arm location remains constant for a given mouse. On day 1, mice are trained for 15 trials (spaced over 3 h), with trials alternating betw...

journal_title：Nature protocols

authors： Alamed J,Wilcock DM,Diamond DM,Gordon MN,Morgan D

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

authors： Koch B,Nijmeijer B,Kueblbeck M,Cai Y,Walther N,Ellenberg J

更新日期：2018-06-01 00:00:00