Volume 17 Issue 6, June 2020

Targeted sequencing perturbations

The cover illustrates targeted Perturb-seq (TAP-seq), which uses a universal PCR handle and gene-specific primers to amplify genes of interest in single cells. TAP-seq boosts the scale and precision of functional genomics screens and uncovers enhancer–target gene interactions at genome scale.

See Schraivogel et al.

Image: illustratoren.de/TobiasWuestefeld. Cover design: Erin Dewalt.

Editorial

Tweet, tweet

We conducted an informal survey to learn how scientists are using Twitter. We share some of the responses and discuss why being active on Twitter offers real benefits.

Editorial 04 Jun 2020

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This Month

Hui Yang

A better base editor with fewer off-target changes, from a die-hard Manchester United fan.

Vivien Marx
This Month 19 May 2020
The SEIRS model for infectious disease dynamics

Realistic models of epidemics account for latency, loss of immunity, births and deaths.

Ottar N. Bjørnstad
Katriona Shea
Naomi Altman
This Month 04 Jun 2020

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Research Highlights

PAM-less is more

Structure-guided engineering allows researchers access to an expanding number of Cas9 variants that relax the constraint imposed by target site recognition of a protospacer-adjacent motif (PAM).

Lei Tang
Research Highlight 04 Jun 2020
Watching embryos develop

Embryonic development is typically hidden from view, but a window preparation technique now sheds light on this phase in the life of a mouse.

Nina Vogt
Research Highlight 04 Jun 2020
Macrophages enter CAR immunotherapy

CAR⁺ macrophages modulate the tumor milieu and lead to antitumor immune responses.

Madhura Mukhopadhyay
Research Highlight 04 Jun 2020
Taxonomy of Bacteria and Archaea

Improvements to the Genome Taxonomy Database provide a complete bacterial and archaeal taxonomy.

Lin Tang
Research Highlight 04 Jun 2020
Chromatin dynamics get mapped

Rita Strack
In Brief 04 Jun 2020
Harmonizing cancer variant knowledgebases

Lin Tang
In Brief 04 Jun 2020
Identifying phosphorylation-site-specific kinases

Arunima Singh
In Brief 04 Jun 2020
A digital embryo

Lei Tang
In Brief 04 Jun 2020
Representation matters for T cell responses

Madhura Mukhopadhyay
In Brief 04 Jun 2020
Optimized tissue clearing

Nina Vogt
In Brief 04 Jun 2020
Mapping DNA single-strand breaks

Lei Tang
In Brief 04 Jun 2020
Fast analysis of single-molecule data

Rita Strack
In Brief 04 Jun 2020
Designing protein logic gates

De novo–designed protein logic gates allow post-translational regulation of protein function.

Arunima Singh
Research Highlight 04 Jun 2020

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Technology Feature

Cell biology befriends soft matter physics

Phase separation creates complex condensates in eukaryotic cells. To study these mysterious droplets, many disciplines come together.

Vivien Marx

Collection:

NatureTech
Technology Feature 20 May 2020

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Review Articles

Scanless two-photon excitation with temporal focusing

This Review discusses temporal focusing microscopy and its applications in neuroscience for imaging and optogenetic activation.

Eirini Papagiakoumou
Emiliano Ronzitti
Valentina Emiliani
Review Article 13 Apr 2020

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Matters Arising

Aggregating transcript-level analyses for single-cell differential gene expression

Etienne Becht
Edward Zhao
Raphael Gottardo
Matters Arising 01 Jun 2020

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Analysis

A comparison of microfluidic methods for high-throughput cell deformability measurements

This Analysis compares microfluidics-based methods for assessing mechanical properties of cells in high throughput.

Marta Urbanska
Hector E. Muñoz
Jochen Guck
Analysis 27 Apr 2020

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Brief Communications

Intelligent image-based deformation-assisted cell sorting with molecular specificity

Sorting RT-FDC combines real-time fluorescence and deformability cytometry with sorting based on standing surface acoustic waves to transfer molecular specificity to label-free, image-based cell sorting using an efficient deep neural network.

Ahmad Ahsan Nawaz
Marta Urbanska
Jochen Guck
Brief Communication 25 May 2020
A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects

Structural and biochemical insights help engineer a cytosine base editor variant that possesses improved on-target activity with minimal DNA and RNA off-target editing.

Erwei Zuo
Yidi Sun
Hui Yang
Brief Communication 18 May 2020
Deep three-photon imaging of the brain in intact adult zebrafish

Three-photon microscopy provides access to most of the adult zebrafish brain for both structural and functional imaging, as well as to the Danionella dracula brain.

Dawnis M. Chow
David Sinefeld
Joseph R. Fetcho
Brief Communication 27 Apr 2020
Elasticizing tissues for reversible shape transformation and accelerated molecular labeling

The ELAST technology renders large tissue samples elastic through embedding in hydrogel and facilitates sample handling and rapid molecular labeling.

Taeyun Ku
Webster Guan
Kwanghun Chung
Brief Communication 18 May 2020

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Articles

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

Souporcell clusters single-cell RNA-seq data using genotype information without the use of a genotype reference.

Haynes Heaton
Arthur M. Talman
Mara K. N. Lawniczak
Article 04 May 2020
Putative cell type discovery from single-cell gene expression data

SCCAF automates the discovery of putative cell types and their feature genes using scRNA-seq data.

Zhichao Miao
Pablo Moreno
Sarah A. Teichmann
Article 18 May 2020
Targeted Perturb-seq enables genome-scale genetic screens in single cells

Targeted sequencing of perturbation effects offers a sensitive approach to capture genes of interest in CRISPR-mediated screens, enabling genome-scale screens at higher scale and lower cost than whole-transcriptome Perturb-seq.

Daniel Schraivogel
Andreas R. Gschwind
Lars M. Steinmetz
Article 01 Jun 2020
Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors

CRISPR-based microraft followed by guide RNA identification (CRaft-ID) combines microraft arrays, microscopy and CRISPR–Cas9 technology for high-content image-based phenotyping. CRaft-ID was used to identify proteins involved in stress granule formation.

Emily C. Wheeler
Anthony Q. Vu
Gene W. Yeo
Article 11 May 2020

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Amendments & Corrections

Publisher Correction: Science in the time of coronavirus

Publisher Correction 27 Apr 2020

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Volume 17 Issue 6, June 2020

Targeted sequencing perturbations

Editorial

This Month

Research Highlights

Technology Feature

Review Articles

Matters Arising

Analysis

Brief Communications

Articles

Amendments & Corrections

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