Quantifying small numbers of antibodies with a 'near-universal' protein-DNA chimera.

abstract：:Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through their 3' untranslated regions, protein-coding RNAs interact with RNA-binding proteins and microRNAs, which regulate many properties, including RNA stability and subcellular localization....

journal_title：Nature methods

authors： Gruber AJ,Gypas F,Riba A,Schmidt R,Zavolan M

更新日期：2018-10-01 00:00:00

abstract：:Methods for genomic analysis at single-cell resolution enable new understanding of complex biological phenomena. Single-cell techniques, ranging from flow cytometry and microfluidics to PCR and sequencing, are used to understand the cellular composition of complex tissues, find new microbial species and perform genome...

journal_title：Nature methods

authors： Kalisky T,Quake SR

更新日期：2011-04-01 00:00:00

abstract：:Spatiotemporal activity patterns in three-dimensionally organized cellular networks are fundamental to the function of the nervous system. Despite advances in functional imaging of cell populations, a method to resolve local network activity in three dimensions has been lacking. Here we introduce a three-dimensional (...

journal_title：Nature methods

authors： Göbel W,Kampa BM,Helmchen F

更新日期：2007-01-01 00:00:00

abstract：:Ribonucleoproteins (RNPs) are key regulators of cellular function. We established an efficient approach, crosslinking of segmentally isotope-labeled RNA and tandem mass spectrometry (CLIR-MS/MS), to localize protein-RNA interactions simultaneously at amino acid and nucleotide resolution. The approach was tested on pol...

journal_title：Nature methods

authors： Dorn G,Leitner A,Boudet J,Campagne S,von Schroetter C,Moursy A,Aebersold R,Allain FH

更新日期：2017-05-01 00:00:00

abstract：:Tumor-initiating cells with stem cell properties are believed to sustain the growth of gliomas, but proposed markers such as CD133 cannot be used to identify these cells with sufficient specificity. We report an alternative isolation method purely based on phenotypic qualities of glioma-initiating cells (GICs), avoidi...

journal_title：Nature methods

authors： Clément V,Marino D,Cudalbu C,Hamou MF,Mlynarik V,de Tribolet N,Dietrich PY,Gruetter R,Hegi ME,Radovanovic I

更新日期：2010-03-01 00:00:00

abstract：:The study of protein-protein interactions by mass spectrometry is an increasingly important part of post-genomics strategies to understand protein function. A variety of mass spectrometry-based approaches allow characterization of cellular protein assemblies under near-physiological conditions and subsequent assignmen...

journal_title：Nature methods

authors： Köcher T,Superti-Furga G

更新日期：2007-10-01 00:00:00

abstract：:Although transcription activator-like effector nucleases (TALENs) can be designed to cleave chosen DNA sequences, TALENs have activity against related off-target sequences. To better understand TALEN specificity, we profiled 30 unique TALENs with different target sites, array length and domain sequences for their abil...

journal_title：Nature methods

authors： Guilinger JP,Pattanayak V,Reyon D,Tsai SQ,Sander JD,Joung JK,Liu DR

更新日期：2014-04-01 00:00:00

abstract：:The complexities of tumor genomes are rapidly being uncovered, but how they are regulated into functional proteomes remains poorly understood. Standard proteomics workflows use databases of known proteins, but these databases do not capture the uniqueness of the cancer transcriptome, with its point mutations, unusual ...

journal_title：Nature methods

authors： Alfaro JA,Sinha A,Kislinger T,Boutros PC

更新日期：2014-11-01 00:00:00

abstract：:Because of ever-increasing throughput requirements of sequencing data, most existing short-read aligners have been designed to focus on speed at the expense of accuracy. The Genome Multitool (GEM) mapper can leverage string matching by filtration to search the alignment space more efficiently, simultaneously deliverin...

journal_title：Nature methods

authors： Marco-Sola S,Sammeth M,Guigó R,Ribeca P

更新日期：2012-12-01 00:00:00

abstract：:Database searching is an essential element of large-scale proteomics. Because these methods are widely used, it is important to understand the rationale of the algorithms. Most algorithms are based on concepts first developed in SEQUEST and PeptideSearch. Four basic approaches are used to determine a match between a s...

journal_title：Nature methods

authors： Sadygov RG,Cociorva D,Yates JR 3rd

更新日期：2004-12-01 00:00:00

abstract：:A quantitative high-throughput FRET-based method of screening fluorescent protein fusion libraries brings the promise of more detailed interactome maps. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2007-02-01 00:00:00

abstract：:Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcomi...

journal_title：Nature methods

authors： Beghin A,Kechkar A,Butler C,Levet F,Cabillic M,Rossier O,Giannone G,Galland R,Choquet D,Sibarita JB

更新日期：2017-12-01 00:00:00

abstract：:We report an atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) setup with a lateral resolution of 1.4 μm, a mass resolution greater than 100,000, and accuracy below ±2 p.p.m. We achieved this by coupling a focusing objective with a numerical aperture (NA) of ...

journal_title：Nature methods

authors： Kompauer M,Heiles S,Spengler B

更新日期：2017-01-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors： Doerr A

更新日期：2019-03-01 00:00:00

abstract：:We have developed a single-plasmid system for the efficient bacterial expression of mutant proteins containing unnatural amino acids at specific sites designated by amber nonsense codons. In this system, multiple copies of a gene encoding an amber suppressor tRNA derived from a Methanocaldococcus jannaschii tyrosyl-tR...

journal_title：Nature methods

authors： Ryu Y,Schultz PG

更新日期：2006-04-01 00:00:00

abstract：:Understanding how cells maintain genome integrity when challenged with DNA double-strand breaks (DSBs) is of major importance, particularly since the discovery of multiple links of DSBs with genome instability and cancer-predisposition disorders. Ionizing radiation is the agent of choice to produce DSBs in cells; howe...

journal_title：Nature methods

authors： Stap J,Krawczyk PM,Van Oven CH,Barendsen GW,Essers J,Kanaar R,Aten JA

更新日期：2008-03-01 00:00:00

abstract：:Recording light-microscopy images of large, nontransparent specimens, such as developing multicellular organisms, is complicated by decreased contrast resulting from light scattering. Early zebrafish development can be captured by standard light-sheet microscopy, but new imaging strategies are required to obtain high-...

journal_title：Nature methods

authors： Keller PJ,Schmidt AD,Santella A,Khairy K,Bao Z,Wittbrodt J,Stelzer EH

更新日期：2010-08-01 00:00:00

abstract：:Caenorhabditis elegans is an important model organism in biology, but until now no antibiotic selection markers have been successfully demonstrated for this species. We have developed a selection system using puromycin that allows the rapid and easy isolation of large populations of transgenic worms. This approach is ...

journal_title：Nature methods

authors： Semple JI,Garcia-Verdugo R,Lehner B

更新日期：2010-09-01 00:00:00

abstract：:We discuss unique features of lens-free computational imaging tools and report some of their emerging results for wide-field on-chip microscopy, such as the achievement of a numerical aperture (NA) of ∼0.8-0.9 across a field of view (FOV) of more than 20 mm(2) or an NA of ∼0.1 across a FOV of ∼18 cm(2), which correspo...

journal_title：Nature methods

authors： Greenbaum A,Luo W,Su TW,Göröcs Z,Xue L,Isikman SO,Coskun AF,Mudanyali O,Ozcan A

更新日期：2012-09-01 00:00:00

abstract：:The importance of locating proteins in their context within cells has been heightened recently by the accomplishments in molecular structure and systems biology. Although light microscopy (LM) has been extensively used for mapping protein localization, many studies require the additional resolution of the electron mic...

journal_title：Nature methods

authors： Giepmans BN,Deerinck TJ,Smarr BL,Jones YZ,Ellisman MH

更新日期：2005-10-01 00:00:00

abstract：:Cell signaling, one of key processes in both normal cellular function and disease, is coordinated by numerous interactions between membrane proteins that change in response to stimuli. We present a split ubiquitin-based method for detection of integral membrane protein-protein interactions (PPIs) in human cells, terme...

journal_title：Nature methods

authors： Petschnigg J,Groisman B,Kotlyar M,Taipale M,Zheng Y,Kurat CF,Sayad A,Sierra JR,Mattiazzi Usaj M,Snider J,Nachman A,Krykbaeva I,Tsao MS,Moffat J,Pawson T,Lindquist S,Jurisica I,Stagljar I

更新日期：2014-05-01 00:00:00

abstract：:The biomedical application of human embryonic stem (hES) cells will increasingly depend on the availability of technologies for highly controlled genetic modification. In mouse genetics, conditional mutagenesis using site-specific recombinases has become an invaluable tool for gain- and loss-of-function studies. Here ...

journal_title：Nature methods

authors： Nolden L,Edenhofer F,Haupt S,Koch P,Wunderlich FT,Siemen H,Brüstle O

更新日期：2006-06-01 00:00:00

abstract：:Phenotype-based small-molecule screening is a powerful method to identify molecules that regulate cellular functions. However, such screens are generally performed in vitro under conditions that do not necessarily model complex physiological conditions or disease states. Here, we use molecular cell barcoding to enable...

journal_title：Nature methods

authors： Grüner BM,Schulze CJ,Yang D,Ogasawara D,Dix MM,Rogers ZN,Chuang CH,McFarland CD,Chiou SH,Brown JM,Cravatt BF,Bogyo M,Winslow MM

更新日期：2016-10-01 00:00:00

abstract：:Numerous drugs and endogenous ligands bind to cell surface receptors leading to modulation of downstream signaling cascades and frequently to adaptation of the plasma membrane proteome. In-depth analysis of dynamic processes at the cell surface is challenging due to biochemical properties and low abundances of plasma ...

journal_title：Nature methods

authors： Kalxdorf M,Günthner I,Becher I,Kurzawa N,Knecht S,Savitski MM,Eberl HC,Bantscheff M

更新日期：2021-01-01 00:00:00

abstract：:Despite widespread use of CRISPR, comprehensive data on the frequency and impact of Cas9-mediated off-targets in modified rodents are limited. Here we present deep-sequencing data from 81 genome-editing projects on mouse and rat genomes at 1,423 predicted off-target sites, 32 of which were confirmed, and show that hig...

journal_title：Nature methods

authors： Anderson KR,Haeussler M,Watanabe C,Janakiraman V,Lund J,Modrusan Z,Stinson J,Bei Q,Buechler A,Yu C,Thamminana SR,Tam L,Sowick MA,Alcantar T,O'Neil N,Li J,Ta L,Lima L,Roose-Girma M,Rairdan X,Durinck S,Warming S

更新日期：2018-07-01 00:00:00

abstract：:The commonly used, monomeric EYFP enabled imaging of intracellular protein structures beyond the optical resolution limit ('super-resolution' imaging) in living cells. By combining photoinduced activation of single EYFP fusions and time-lapse imaging, we obtained sub-40 nm resolution images of the filamentous superstr...

journal_title：Nature methods

authors： Biteen JS,Thompson MA,Tselentis NK,Bowman GR,Shapiro L,Moerner WE

更新日期：2008-11-01 00:00:00

abstract：:To enable the detection of expression signatures specific to individual cells, we developed PLAYR (proximity ligation assay for RNA), a method for highly multiplexed transcript quantification by flow and mass cytometry that is compatible with standard antibody staining. When used with mass cytometry, PLAYR allowed for...

journal_title：Nature methods

authors： Frei AP,Bava FA,Zunder ER,Hsieh EW,Chen SY,Nolan GP,Gherardini PF

更新日期：2016-03-01 00:00:00

abstract：:An uncharged CoA precursor that can enter the cell is used for covalent, site-specific labeling of proteins inside living cells. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2006-11-01 00:00:00

abstract：:Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active-site conformations and consequently alter protein function. Observing alternative conformations at low levels of electron density, in addition to comparison of in...

journal_title：Nature methods

authors： van den Bedem H,Bhabha G,Yang K,Wright PE,Fraser JS

更新日期：2013-09-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors： Vogt N

更新日期：2019-02-01 00:00:00