Publisher Correction: PEG-4MAL hydrogels for human organoid generation, culture, and in vivo delivery.

Abstract:

:In the version of this protocol originally published, the caption for Fig. 3 was erroneously placed with Fig. 4, and that for Fig. 4 was placed with Fig. 3. This error has been corrected in the HTML and PDF versions of the paper.

journal_name

Nat Protoc

journal_title

Nature protocols

authors

Cruz-Acuña R,Quirós M,Huang S,Siuda D,Spence JR,Nusrat A,García AJ

doi

10.1038/s41596-018-0079-5

subject

Has Abstract

pub_date

2019-07-01 00:00:00

pages

2258

issue

7

eissn

1754-2189

issn

1750-2799

pii

10.1038/s41596-018-0079-5

journal_volume

14

pub_type

已发布勘误
  • Synthesis of alkyl- and aryl-amino-substituted anthraquinone derivatives by microwave-assisted copper(0)-catalyzed Ullmann coupling reactions.

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2010.63

    authors: Baqi Y,Müller CE

    更新日期:2010-05-01 00:00:00

  • Self-assembly and characterization of 2D plasmene nanosheets.

    abstract::Freestanding plasmonic nanoparticle (NP) superlattice sheets are novel 2D nanomaterials with tailorable properties that enable their use for broad applications in sensing, anticounterfeit measures, ionic gating, nanophotonics and flat lenses. We recently developed a robust, yet general, two-step drying-mediated approa...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0200-4

    authors: Dong D,Fu R,Shi Q,Cheng W

    更新日期:2019-09-01 00:00:00

  • Microwave-assisted synthesis of triple-helical, collagen-mimetic lipopeptides.

    abstract::Collagen-mimetic peptides and lipopeptides are widely used as substrates for matrix degrading enzymes, as new biomaterials for tissue engineering, as drug delivery systems and so on. However, the preparation and subsequent purification of these peptides and their fatty-acid conjugates are really challenging. Herein, w...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.195

    authors: Banerjee J,Hanson AJ,Muhonen WW,Shabb JB,Mallik S

    更新日期:2010-01-01 00:00:00

  • Cryopreservation and banking of mammalian cell lines.

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.190

    authors: Stacey GN,Masters JR

    更新日期:2008-01-01 00:00:00

  • Preparation, functionalization and characterization of engineered carbon nanodots.

    abstract::Carbon-based dots (CDs) and their functionalized (nano)composites have recently attracted attention due to their seemingly easy preparation and numerous potential applications, ranging from those in the biomedical field (i.e., imaging and drug delivery) to those in (opto)electronics (i.e., solar cells and LEDs). This ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0207-x

    authors: Ðorđević L,Arcudi F,Prato M

    更新日期:2019-10-01 00:00:00

  • Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.101

    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

  • Langmuir-Blodgett nanotemplates for protein crystallography.

    abstract::The new generation of synchrotrons and microfocused beamlines has enabled great progress in X-ray protein crystallography, resulting in new 3D atomic structures for proteins of high interest to the pharmaceutical industry and life sciences. It is, however, often still challenging to produce protein crystals of suffici...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2017.108

    authors: Pechkova E,Nicolini C

    更新日期:2017-12-01 00:00:00

  • MicroRNA detection by northern blotting using locked nucleic acid probes.

    abstract::MicroRNAs (miRNAs) are short, about 21 nucleotides in length, noncoding, regulatory RNA molecules representing a new layer in post-transcriptional regulation of gene expression. Intensive miRNA research has necessitated the development of effective miRNA detection methods such as northern analyses, quantitative real-t...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.528

    authors: Várallyay E,Burgyán J,Havelda Z

    更新日期:2008-01-01 00:00:00

  • Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing.

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2018.042

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

    更新日期:2018-06-01 00:00:00

  • Site-specific protein labeling using PRIME and chelation-assisted click chemistry.

    abstract::This protocol describes an efficient method to site-specifically label cell-surface or purified proteins with chemical probes in two steps: probe incorporation mediated by enzymes (PRIME) followed by chelation-assisted copper-catalyzed azide-alkyne cycloaddition (CuAAC). In the PRIME step, Escherichia coli lipoic acid...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.096

    authors: Uttamapinant C,Sanchez MI,Liu DS,Yao JZ,Ting AY

    更新日期:2013-08-01 00:00:00

  • Frozen competent yeast cells that can be transformed with high efficiency using the LiAc/SS carrier DNA/PEG method.

    abstract::Here we describe a protocol for the production of frozen competent yeast cells that can be transformed with high efficiency using the lithium acetate/single-stranded carrier DNA/PEG method. This protocol allows the production of highly competent yeast cells that can be frozen and used at a later date and is especially...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.17

    authors: Gietz RD,Schiestl RH

    更新日期:2007-01-01 00:00:00

  • Fast and easy phosphopeptide fractionation by combinatorial ERLIC-SCX solid-phase extraction for in-depth phosphoproteome analysis.

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.134

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

    更新日期:2016-01-01 00:00:00

  • 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2012.005

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

    更新日期:2012-02-23 00:00:00

  • A rapid micro chromatin immunoprecipitation assay (microChIP).

    abstract::Interactions of proteins with DNA mediate many critical nuclear functions. Chromatin immunoprecipitation (ChIP) is a robust technique for studying protein-DNA interactions. Current ChIP assays, however, either require large cell numbers, which prevent their application to rare cell samples or small-tissue biopsies, or...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.68

    authors: Dahl JA,Collas P

    更新日期:2008-01-01 00:00:00

  • Standardization of complex biologically derived spectrochemical datasets.

    abstract::Spectroscopic techniques such as Fourier-transform infrared (FTIR) spectroscopy are used to study interactions of light with biological materials. This interaction forms the basis of many analytical assays used in disease screening/diagnosis, microbiological studies, and forensic/environmental investigations. Advantag...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0150-x

    authors: Morais CLM,Paraskevaidi M,Cui L,Fullwood NJ,Isabelle M,Lima KMG,Martin-Hirsch PL,Sreedhar H,Trevisan J,Walsh MJ,Zhang D,Zhu YG,Martin FL

    更新日期:2019-05-01 00:00:00

  • In vitro 'sexual' evolution through the PCR-based staggered extension process (StEP).

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.309

    authors: Zhao H,Zha W

    更新日期:2006-01-01 00:00:00

  • Micropatterning of living cells by laser-guided direct writing: application to fabrication of hepatic-endothelial sinusoid-like structures.

    abstract::Here, we describe a simple protocol for the design and construction of a laser-guided direct writing (LGDW) system able to micropattern the self-assembly of liver sinusoid-like structures with micrometer resolution in vitro. To the best of our knowledge, LGDW is the only technique able to pattern cells "on the fly" wi...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.386

    authors: Nahmias Y,Odde DJ

    更新日期:2006-01-01 00:00:00

  • Understanding chemical reactivity using the activation strain model.

    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

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0265-0

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

    更新日期:2020-02-01 00:00:00

  • Characterization of bacterial spore germination using phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers.

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2011.307

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

    更新日期:2011-05-01 00:00:00

  • Simultaneous analysis of reactive oxygen species and reduced glutathione content in living cells by polychromatic flow cytometry.

    abstract::Reactive oxygen species (ROS) are continuously produced in the cell as a consequence of aerobic metabolism, and are controlled by several antioxidant mechanisms. An accurate measurement of ROS is essential to evaluate the redox status of the cell, or the effects of molecules with the pro-oxidant or antioxidant activit...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.189

    authors: Cossarizza A,Ferraresi R,Troiano L,Roat E,Gibellini L,Bertoncelli L,Nasi M,Pinti M

    更新日期:2009-01-01 00:00:00

  • Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2.

    abstract::This protocol describes a method to obtain spatially resolved proteomic maps of specific compartments within living mammalian cells. An engineered peroxidase, APEX2, is genetically targeted to a cellular region of interest. Upon the addition of hydrogen peroxide for 1 min to cells preloaded with a biotin-phenol substr...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2016.018

    authors: Hung V,Udeshi ND,Lam SS,Loh KH,Cox KJ,Pedram K,Carr SA,Ting AY

    更新日期:2016-03-01 00:00:00

  • ADP-ribose-specific chromatin-affinity purification for investigating genome-wide or locus-specific chromatin ADP-ribosylation.

    abstract::Protein ADP-ribosylation is a structurally heterogeneous post-translational modification (PTM) that influences the physicochemical and biological properties of the modified protein. ADP-ribosylation of chromatin changes its structural properties, thereby regulating important nuclear functions. A lack of suitable antib...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2017.072

    authors: Bisceglie L,Bartolomei G,Hottiger MO

    更新日期:2017-09-01 00:00:00

  • Gel-based mass spectrometric analysis of a strongly hydrophobic GABAA-receptor subunit containing four transmembrane domains.

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.92

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

    更新日期:2009-01-01 00:00:00

  • TARDIS, a targeted RNA directional sequencing method for rare RNA discovery.

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.120

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

    更新日期:2015-12-01 00:00:00

  • High-yield and high-purity isolation of hepatic stellate cells from normal and fibrotic mouse livers.

    abstract::Hepatic stellate cells (HSCs) have been identified as the main fibrogenic cell type in the liver. Hence, efforts to understand hepatic fibrogenesis and to develop treatment strategies have focused on this cell type. HSC isolation, originally developed in rats, has subsequently been adapted to mice, thus allowing the s...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.017

    authors: Mederacke I,Dapito DH,Affò S,Uchinami H,Schwabe RF

    更新日期:2015-02-01 00:00:00

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

    abstract::Blood circulating endothelial cells (CECs) and circulating hematopoietic progenitor cells (CPCs) represent two cell populations that are thought to play important roles in tissue vascularization. CECs and CPCs are currently studied as surrogate markers in patients for more than a dozen pathologies, including heart dis...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.111

    authors: Duda DG,Cohen KS,Scadden DT,Jain RK

    更新日期:2007-01-01 00:00:00

  • Synthesis of an ultrasensitive BODIPY-derived fluorescent probe for detecting HOCl in live cells.

    abstract::Hypochlorous acid (HOCl) is a critical member of the reactive oxygen species (ROS) produced by immune cells to fight infections. On the other hand, HOCl in homeostasis causes oxidative damage to biomolecules and is linked to many diseases, including inflammatory, neurodegenerative, and cardiovascular diseases. Herein,...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-018-0041-6

    authors: Zhu H,Zhang Z,Long S,Du J,Fan J,Peng X

    更新日期:2018-10-01 00:00:00

  • Target analysis by integration of transcriptome and ChIP-seq data with BETA.

    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

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.150

    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

  • Analysis of mutational spectra by denaturing capillary electrophoresis.

    abstract::The point mutational spectrum over nearly any 75- to 250-bp DNA sequence isolated from cells, tissues or large populations may be discovered using denaturing capillary electrophoresis (DCE). A modification of the standard DCE method that uses cycling temperature (e.g., +/-5 degrees C), CyDCE, permits optimal resolutio...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.79

    authors: Ekstrøm PO,Khrapko K,Li-Sucholeiki XC,Hunter IW,Thilly WG

    更新日期:2008-01-01 00:00:00

  • Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification.

    abstract::Activity-based protein profiling (ABPP) has emerged as a valuable chemical proteomics method to guide the therapeutic development of covalent drugs by assessing their on-target engagement and off-target activity. We recently used ABPP to determine the serine hydrolase interaction landscape of the experimental drug BIA...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2017.159

    authors: van Rooden EJ,Florea BI,Deng H,Baggelaar MP,van Esbroeck ACM,Zhou J,Overkleeft HS,van der Stelt M

    更新日期:2018-04-01 00:00:00