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University Imaging Centers - Where the University sees the future

Journal Articles

Multicolor quantitative confocal imaging cytometry

Nature Methods - 13 November 2017 - 12:00am

Multicolor quantitative confocal imaging cytometry

Multicolor quantitative confocal imaging cytometry, Published online: 13 November 2017; doi:10.1038/nmeth.4503

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This resource paper describes the steps involved in carrying out quantitative multicolour imaging in tissue. It is applied to cleared mouse bone and plots the spatial distribution of specific cell populations within the marrow.

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Categories: Journal Articles

Profiling the transcriptome with RNA SPOTs

Nature Methods - 13 November 2017 - 12:00am

Profiling the transcriptome with RNA SPOTs

Profiling the transcriptome with RNA SPOTs, Published online: 13 November 2017; doi:10.1038/nmeth.4500

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RNA SPOTs adapts sequential fluorescence in situ hybridization (seqFISH) for highly accurate and inexpensive transcriptome-scale or targeted RNA quantification in vitro.

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Categories: Journal Articles

An improved MS2 system for accurate reporting of the mRNA life cycle

Nature Methods - 13 November 2017 - 12:00am

An improved MS2 system for accurate reporting of the mRNA life cycle

An improved MS2 system for accurate reporting of the mRNA life cycle, Published online: 13 November 2017; doi:10.1038/nmeth.4502

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An improved MS2-tagging system for live-cell RNA imaging allows faithful monitoring of the mRNA life cycle, overcoming degradation artifacts associated with previous versions and having implications regarding mRNA regulation in yeast.

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Categories: Journal Articles

The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power

Nature Methods - 13 November 2017 - 12:00am

The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power

The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power, Published online: 13 November 2017; doi:10.1038/nmeth.4504

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The high spatial resolution of secondary ion mass spectrometry and the high resolving power of the Orbitrap mass spectrometer are combined in a single imaging platform, the 3D OrbiSIMS. The instrument's capabilities for resolving lipids and neurotransmitters in the brain with subcellular spatial resolution, and a drug in a single cell in three dimensions is demonstrated.

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Categories: Journal Articles

Isolation and 3D expansion of multipotent Sox9<sup>+</sup> mouse lung progenitors

Nature Methods - 6 November 2017 - 12:00am

Isolation and 3D expansion of multipotent Sox9+ mouse lung progenitors

Isolation and 3D expansion of multipotent Sox9<sup>+</sup> mouse lung progenitors, Published online: 06 November 2017; doi:10.1038/nmeth.4498

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This paper describes methods for the 3D culture of mouse lung progenitor cells that can differentiate in vitro and in vivo along all epithelial lineages.

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Categories: Journal Articles

The Author File: Alice C. McHardy

Nature Methods - 31 October 2017 - 12:00am

The Author File: Alice C. McHardy

The Author File: Alice C. McHardy, Published online: 31 October 2017; doi:10.1038/nmeth.4485

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How to run a computational competition energized by modern dance.

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Categories: Journal Articles

DNA sequencing: Packing, trapping and sequencing

Nature Methods - 31 October 2017 - 12:00am

DNA sequencing: Packing, trapping and sequencing

DNA sequencing: Packing, trapping and sequencing, Published online: 31 October 2017; doi:10.1038/nmeth.4487

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Ultralow concentrations of DNA can be optically sequenced with SMRT DNA sequencing.

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Categories: Journal Articles

Stem cells: Antibodies trigger reprogramming

Nature Methods - 31 October 2017 - 12:00am

Stem cells: Antibodies trigger reprogramming

Stem cells: Antibodies trigger reprogramming, Published online: 31 October 2017; doi:10.1038/nmeth.4491

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Antibodies that initiate signaling cascades and thereby replace reprogramming factors promise an efficient and safe way to produce pluripotent stem cells.

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Categories: Journal Articles

Microscopy: Laser-emission microscopy

Nature Methods - 31 October 2017 - 12:00am

Microscopy: Laser-emission microscopy

Microscopy: Laser-emission microscopy, Published online: 31 October 2017; doi:10.1038/nmeth.4489

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An optical setup for observing targeted fluorophores lasing from within tissue.

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Categories: Journal Articles

Genomics: A function-first look at tumor heterogeneity

Nature Methods - 31 October 2017 - 12:00am

Genomics: A function-first look at tumor heterogeneity

Genomics: A function-first look at tumor heterogeneity, Published online: 31 October 2017; doi:10.1038/nmeth.4493

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Fate maps of human brain cancer cells, transplanted in mouse, challenge traditional views of tumor genomic heterogeneity.

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Categories: Journal Articles

Accessible, curated metagenomic data through ExperimentHub

Nature Methods - 31 October 2017 - 12:00am

Accessible, curated metagenomic data through ExperimentHub

Accessible, curated metagenomic data through ExperimentHub, Published online: 31 October 2017; doi:10.1038/nmeth.4468

Categories: Journal Articles

Neurobiology: gene expression captured on-site

Nature Methods - 31 October 2017 - 12:00am

Neurobiology: gene expression captured on-site

Neurobiology: gene expression captured on-site, Published online: 31 October 2017; doi:10.1038/nmeth.4472

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A wealth of spatial techniques capture the 'where' of gene expression.

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Categories: Journal Articles

Localization-based super-resolution imaging meets high-content screening

Nature Methods - 30 October 2017 - 12:00am

Localization-based super-resolution imaging meets high-content screening

Nature Methods, Published online: 30 October 2017; doi:10.1038/nmeth.4486

An automated system for data acquisition and analysis enables high-content screening localization microscopy and increases the throughput and information content of super-resolution microscopy methods such as dSTORM, DNA-PAINT and (spt)PALM.

Categories: Journal Articles

An objective comparison of cell-tracking algorithms

Nature Methods - 30 October 2017 - 12:00am

An objective comparison of cell-tracking algorithms

Nature Methods, Published online: 30 October 2017; doi:10.1038/nmeth.4473

This analysis describes the results of three Cell Tracking Challenge editions for examining the performance of cell segmentation and tracking algorithms and provides practical feedback for users and developers.

Categories: Journal Articles

Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factors

Nature Methods - 30 October 2017 - 12:00am

Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factors

Nature Methods, Published online: 30 October 2017; doi:10.1038/nmeth.4483

Inducible dCpf1-based transcriptional activators achieve tunable, multiplexed target gene expression.

Categories: Journal Articles

High-throughput, image-based screening of pooled genetic-variant libraries

Nature Methods - 30 October 2017 - 12:00am

High-throughput, image-based screening of pooled genetic-variant libraries

Nature Methods, Published online: 30 October 2017; doi:10.1038/nmeth.4495

Multiplexed FISH readout of barcoded genotypes in single cells allows pooled screening of large genetic-variant libraries for complex, image-based phenotypes.

Categories: Journal Articles

Deciphering lipid structures based on platform-independent decision rules

Nature Methods - 23 October 2017 - 12:00am

Deciphering lipid structures based on platform-independent decision rules

Nature Methods, Published online: 23 October 2017; doi:10.1038/nmeth.4470

The Lipid Data Analyzer uses sets of decision rules to identify lipid subclasses in high-throughput LC-MS/MS data.

Categories: Journal Articles

Antibodies to biotin enable large-scale detection of biotinylation sites on proteins

Nature Methods - 16 October 2017 - 12:00am

Antibodies to biotin enable large-scale detection of biotinylation sites on proteins

Nature Methods, Published online: 16 October 2017; doi:10.1038/nmeth.4465

Enrichment of biotinylated peptides using an anti-biotin antibody results in substantially improved biotinylation site identifications by mass spectrometry compared to traditional streptavidin-based biotinylated protein enrichment.

Categories: Journal Articles

Rapid nonlinear image scanning microscopy

Nature Methods - 16 October 2017 - 12:00am

Rapid nonlinear image scanning microscopy

Nature Methods, Published online: 16 October 2017; doi:10.1038/nmeth.4467

A rescanning microscopy approach enables two-photon image-scanning microscopy that doubles resolution relative to that of conventional two-photon microscopy at high frame rates and with high sensitivity for improved super-resolution imaging of living specimens.

Categories: Journal Articles

Protein interaction perturbation profiling at amino-acid resolution

Nature Methods - 16 October 2017 - 12:00am

Protein interaction perturbation profiling at amino-acid resolution

Nature Methods, Published online: 16 October 2017; doi:10.1038/nmeth.4464

A reverse two-hybrid approach combined with massively parallel programmed mutagenesis and sequencing allows profiling protein interaction determinants at amino-acid resolution, as demonstrated by identifying interaction-disrupting mutations in a cilia protein complex associated with Bardet–Biedl syndrome.

Categories: Journal Articles

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