In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples.

abstract：:Here, we describe a simple micromolding method to construct three-dimensional arrays of organotypic epithelial tissue structures that approximate in vivo histology. An elastomeric stamp containing an array of posts of defined geometry and spacing is used to mold microscale cavities into the surface of type I collagen ...

journal_title：Nature protocols

authors： Nelson CM,Inman JL,Bissell MJ

更新日期：2008-01-01 00:00:00

abstract：:'Adult' or 'somatic' stem cells harbor an intrinsic ability to regenerate tissues. Heterogeneity of such stem cells along the gastrointestinal tract yields the known segmental specificity of this organ and may contribute to the pathology of certain enteric conditions. Here we detail technology for the generation of 'l...

journal_title：Nature protocols

authors： Duleba M,Yamamoto Y,Neupane R,Rao W,Xie J,Qi Y,Liew AA,Niroula S,Zhang Y,Mahalingam R,Wang S,Goller K,Ajani JA,Vincent M,Ho KY,Hou JK,Hyams JS,Sylvester FA,Crum CP,McKeon F,Xian W

更新日期：2020-05-01 00:00:00

abstract：:Hi-C is a powerful method that provides pairwise information on genomic regions in spatial proximity in the nucleus. Hi-C requires millions of cells as input and, as genome organization varies from cell to cell, a limitation of Hi-C is that it only provides a population average of genome conformations. We developed si...

journal_title：Nature protocols

authors： Nagano T,Lubling Y,Yaffe E,Wingett SW,Dean W,Tanay A,Fraser P

更新日期：2015-12-01 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：: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：:Here we present a protocol for labeling aliphatic carboxylic acids with the positron-emitting radionuclide 11C (t(1/2) = 20.4 min) at the carboxyl position using [11C]carbon monoxide via photoinitiated free radical-mediated carbonylation. A solution of an alkyl iodide in a homogenous binary organic solvent-water mixtu...

journal_title：Nature protocols

authors： Itsenko O,Kihlberg T,Långström B

更新日期：2006-01-01 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：:Over the past 20 years, the starlet sea anemone, Nematostella vectensis, a small estuarine animal, has emerged as a powerful model system for field and laboratory studies of development, evolution, genomics, molecular biology and toxicology. Here we describe how to collect Nematostella, culture it through its entire s...

journal_title：Nature protocols

authors： Stefanik DJ,Friedman LE,Finnerty JR

更新日期：2013-05-01 00:00:00

abstract：:This protocol describes a directed evolution method for in vitro mutagenesis and recombination of polynucleotide sequences. The staggered extension process (StEP) is essentially a modified PCR that uses highly abbreviated annealing and extension steps to generate staggered DNA fragments and promote crossover events al...

journal_title：Nature protocols

authors： Zhao H,Zha W

更新日期：2006-01-01 00:00:00

abstract：:Top-down proteomics (TDP) by mass spectrometry (MS) is a technique by which intact proteins are analyzed. It has become increasingly popDesalting and concentrating GELFrEEular in translational research because of the value of characterizing distinct proteoforms of intact proteins. Compared to bottom-up proteomics (BUP...

journal_title：Nature protocols

authors： Toby TK,Fornelli L,Srzentić K,DeHart CJ,Levitsky J,Friedewald J,Kelleher NL

更新日期：2019-01-01 00:00:00

abstract：:The fabrication of 3D tissues retaining the original functions of tissues/organs in vitro is crucial for optimal tissue engineering and regenerative medicine. The fabrication of 3D tissues also contributes to the establishment of in vitro tissue/organ models for drug screening. Our laboratory has developed a fabricati...

journal_title：Nature protocols

authors： Haraguchi Y,Shimizu T,Sasagawa T,Sekine H,Sakaguchi K,Kikuchi T,Sekine W,Sekiya S,Yamato M,Umezu M,Okano T

更新日期：2012-04-05 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：: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：: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：:Cap-analysis gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. CAGE allows mapping of all the initiation sites of both capped coding and noncoding RNAs. In addition, transcriptional start sites within promoters are characterized at single-nucleotide resolution. The latter allows t...

journal_title：Nature protocols

authors： Takahashi H,Lassmann T,Murata M,Carninci P

更新日期：2012-02-23 00:00:00

abstract：:The mouse embryo hindbrain is a robust and adaptable model for studying sprouting angiogenesis. It permits the spatiotemporal analysis of organ vascularization in normal mice and in mouse strains with genetic mutations that result in late embryonic or perinatal lethality. Unlike postnatal models such as retinal angiog...

journal_title：Nature protocols

authors： Fantin A,Vieira JM,Plein A,Maden CH,Ruhrberg C

更新日期：2013-02-01 00:00:00

abstract：:Cell migration is a key feature of virtually every biological process, and it can be studied in a variety of ways. Here we outline a protocol for the in vitro study of cell migration using a ring barrier-based assay. A 'barrier' is inserted in the culture chamber, which prevents cells from entering a defined area. Cel...

journal_title：Nature protocols

authors： Das AM,Eggermont AM,ten Hagen TL

更新日期：2015-06-01 00:00:00

abstract：:The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression. Several recently published methods combine transcription factor (TF) binding and gene expression for target prediction, but few of them provide an efficient software package for the community. ...

journal_title：Nature protocols

authors： Wang S,Sun H,Ma J,Zang C,Wang C,Wang J,Tang Q,Meyer CA,Zhang Y,Liu XS

更新日期：2013-12-01 00:00:00

abstract：:Cyclodepsipeptides are cyclic peptides in which at least one amide link on the backbone is replaced with an ester link. These natural products present a high structural diversity that corresponds to a broad range of biological activities. Therefore, they are very promising pharmaceutical candidates. Most of the cyclod...

journal_title：Nature protocols

authors： Pelay-Gimeno M,Albericio F,Tulla-Puche J

更新日期：2016-10-01 00:00:00

abstract：:This transformation procedure generates, with high efficiency (70-90%), hairy roots in cultivars, landraces and accessions of Phaseolus vulgaris (common bean) and other Phaseolus spp. Hairy roots rapidly develop after wounding young plantlets with Agrobacterium rhizogenes, at the cotyledon node, and keeping the plants...

journal_title：Nature protocols

authors： Estrada-Navarrete G,Alvarado-Affantranger X,Olivares JE,Guillén G,Díaz-Camino C,Campos F,Quinto C,Gresshoff PM,Sanchez F

更新日期：2007-01-01 00:00:00

abstract：:This protocol describes the primary culture of individual chromaffin cells derived by enzymatic digestion from the adrenal medulla of the bovine adrenal gland. Since the late 1970s, such cells have provided a useful model system to study neurotransmitter biosynthesis, storage and release in the catecholaminergic syste...

journal_title：Nature protocols

authors： O'Connor DT,Mahata SK,Mahata M,Jiang Q,Hook VY,Taupenot L

更新日期：2007-01-01 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 is a critical factor in AIDS and other viral illnesses, cerebral and myocardial ischemia, autoimmune and neurodegenerative states, organ and bone marrow transplant rejection, and tumor response to chemotherapy and radiation. Improved methods to identify sites of apoptosis are increasing our understanding of ...

journal_title：Nature protocols

authors： Blankenberg FG,Vanderheyden JL,Strauss HW,Tait JF

更新日期：2006-01-01 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：:The immune system operates at the scale of the whole organism in mammals. We currently lack experimental approaches to systematically track and study organism-wide molecular processes in mice. Here we describe an integrated toolkit for measuring gene expression in whole tissues, 3-prime mRNA extension sequencing, that...

journal_title：Nature protocols

authors： Pandey S,Takahama M,Gruenbaum A,Zewde M,Cheronis K,Chevrier N

更新日期：2020-04-01 00:00:00

abstract：:Efforts to cure HIV are hampered by limited characterization of the cells supporting HIV replication in vivo and inadequate methods for quantifying the latent viral reservoir in individuals receiving antiretroviral therapy (ART). We describe a protocol for flow cytometric identification of viral reservoirs, based on c...

journal_title：Nature protocols

authors： Baxter AE,Niessl J,Fromentin R,Richard J,Porichis F,Massanella M,Brassard N,Alsahafi N,Routy JP,Finzi A,Chomont N,Kaufmann DE

更新日期：2017-10-01 00:00:00

abstract：:Protein digestion using a dedicated protease represents a key element in a typical mass spectrometry (MS)-based shotgun proteomics experiment. Up to now, digestion has been predominantly performed with trypsin, mainly because of its high specificity, widespread availability and ease of use. Lately, it has become appar...

journal_title：Nature protocols

authors： Giansanti P,Tsiatsiani L,Low TY,Heck AJ

更新日期：2016-05-01 00:00:00

abstract：:The forced swim test (FST) is one of the most commonly used animal models for assessing antidepressant-like behavior. This protocol details using the FST in rats, which takes place over 48 h and is followed by the video analysis of the behavior. The swim test involves the scoring of active (swimming and climbing) or p...

journal_title：Nature protocols

authors： Slattery DA,Cryan JF

更新日期：2012-05-03 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：: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