Tuesday, May 30, 2017

Nature Methods Contents: June 2017 Volume 14 pp 541 - 635

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TABLE OF CONTENTS

June 2017 Volume 14, Issue 6

In This Issue
Editorial
This Month
Correspondence
Research Highlights
Technology Feature
News and Views
Perspective
Brief Communications
Articles
Application Note
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In This Issue

Top

In This Issue   

 

Editorial

Top

CRISPR standards   p541
doi:10.1038/nmeth.4328
With the ever-expanding use of CRISPR technology, the development of standards to quantitatively benchmark on- and off-target activity needs to keep pace.

 

This Month

Top

The Author File: Yannick Doyon   p543
Vivien Marx
doi:10.1038/nmeth.4296
Teamwork on and off the ice, and tipping the odds to find CRISPR hits sans markers.

 

Points of Significance: Clustering   pp545 - 546
Naomi Altman and Martin Krzywinski
doi:10.1038/nmeth.4299
Clustering finds patterns in data—whether they are there or not.

 

Correspondence

Top

Unexpected mutations after CRISPR-Cas9 editing in vivo   pp547 - 548
Kellie A Schaefer, Wen-Hsuan Wu, Diana F Colgan, Stephen H Tsang, Alexander G Bassuk et al.
doi:10.1038/nmeth.4293

 

Digenome-seq web tool for profiling CRISPR specificity   pp548 - 549
Jeongbin Park, Liam Childs, Daesik Kim, Gue-Ho Hwang, Sunghyun Kim et al.
doi:10.1038/nmeth.4262

 

E-scape: interactive visualization of single-cell phylogenetics and cancer evolution   pp549 - 550
Maia A Smith, Cydney B Nielsen, Fong Chun Chan, Andrew McPherson, Andrew Roth et al.
doi:10.1038/nmeth.4303

 

Research Highlights

Top

GPCR interactions in space and time
A proximity labeling technique yields new insights into GPCR signaling.

Good vibrations for super-multiplexed imaging
Researchers optimize stimulated Raman scattering microscopy and combine it with a new panel of Raman-active dyes to enable 24-color bioimaging.

CRISPR's paper test
A spot of CRISPR protein on paper provides a powerful diagnostic assay.

Extending pluripotency with a cocktail
A chemical combination enables culture of pluripotent cells.

Microfetti: a fate-mapping system for microglia
A multicolor reporter mouse model enables monitoring of the fate and dynamics of microglia in health and disease.

Methods in Brief

Engineering complex and robust genetic circuits | Track first and identify later | Single genome amplification goes linear | Chip-based nanoscopy

Tools in Brief

GPCR function insights by cryo-EM | Deep learning improves image analysis | Building a better TRAP for translation | Electrophysiology in intact Caenorhabditis elegans

Methods
JOBS of the week
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Technology Feature

Top

Organoids: a better in vitro model   pp559 - 562
Katherine Ellen Foley
doi:10.1038/nmeth.4307
3D human cell cultures are changing the way scientists model organ development and function—but they have their own set of complications.

 

News and Views

Top

Cas9 in action: no more known unknowns?   pp563 - 564
Fyodor D Urnov
doi:10.1038/nmeth.4301
Useful new methods are being introduced to experimentally determine the genome-wide consequences of Cas9-based editing.

See also: Article by Cameron et al. | Article by Tsai et al.

 

Perspective

Top

Normalizing single-cell RNA sequencing data: challenges and opportunities   pp565 - 571
Catalina A Vallejos, Davide Risso, Antonio Scialdone, Sandrine Dudoit and John C Marioni
doi:10.1038/nmeth.4292
This Perspective examines single-cell RNA-seq data challenges and the need for normalization methods designed specifically for single-cell data in order to remove technical biases.

 

Brief Communications

Top

Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions   pp573 - 576
John Paul Shen, Dongxin Zhao, Roman Sasik, Jens Luebeck, Amanda Birmingham et al.
doi:10.1038/nmeth.4225
A library of plasmids expressing two gRNAs allows for the mapping of combinatorial genetic interactions with the CRISPR system. Results in cancer cells suggest that cellular context is an important factor for the interaction network.

 

Genetic interaction mapping in mammalian cells using CRISPR interference   pp577 - 580
Dan Du, Assen Roguev, David E Gordon, Meng Chen, Si-Han Chen et al.
doi:10.1038/nmeth.4286
CRISPR interference screens with pairs of sgRNAs allow for quantitative characterization of genetic interactions.

 

Large-field-of-view imaging by multi-pupil adaptive optics   pp581 - 583
Jung-Hoon Park, Lingjie Kong, Yifeng Zhou and Meng Cui
doi:10.1038/nmeth.4290
Adaptive optics can counteract optical aberrations within tissues, but the field of view is typically limited. Multi-pupil adaptive optics expands the area that can be imaged, and this is demonstrated by multiple applications in the mouse brain imaging.

 

SCnorm: robust normalization of single-cell RNA-seq data   pp584 - 586
Rhonda Bacher, Li-Fang Chu, Ning Leng, Audrey P Gasch, James A Thomson et al.
doi:10.1038/nmeth.4263
SCnorm normalizes single-cell RNA-seq data for improved downstream analyses such as differential expression and cell-state discrimination.

 

ModelFinder: fast model selection for accurate phylogenetic estimates   pp587 - 589
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler and Lars S Jermiin
doi:10.1038/nmeth.4285
ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates.

 

Genome-wide profiling of heritable and de novo STR variations   pp590 - 592
Thomas Willems, Dina Zielinski, Jie Yuan, Assaf Gordon, Melissa Gymrek et al.
doi:10.1038/nmeth.4267
HipSTR accurately genotypes and phases short tandem repeats, enabling robust genome-wide analyses of short tandem repeat variations.

 
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Articles

Top

Iterative expansion microscopy   pp593 - 599
Jae-Byum Chang, Fei Chen, Young-Gyu Yoon, Erica E Jung, Hazen Babcock et al.
doi:10.1038/nmeth.4261
Iterative expansion microscopy (iExM) is a strategy that achieves high resolution expansion microscopy by expanding samples multiple times. Expanding a sample twice enables ∼4.5 × 4.5 ∼20× physical expansion and ∼25 nm resolution.

 

Mapping the genomic landscape of CRISPR-Cas9 cleavage   pp600 - 606
Peter Cameron, Chris K Fuller, Paul D Donohoue, Brittnee N Jones, Matthew S Thompson et al.
doi:10.1038/nmeth.4284
SITE-Seq probes Cas9 cleavage sites in vitro and returns a comprehensive list of off-target sites at different Cas9-sgRNA concentrations.

See also: News and Views by Urnov

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets   pp607 - 614
Shengdar Q Tsai, Nhu T Nguyen, Jose Malagon-Lopez, Ved V Topkar, Martin J Aryee et al.
doi:10.1038/nmeth.4278
CIRCLE-seq is an in vitro assay for selectively sequencing off-target sites cleaved by Cas9-sgRNA in genomic DNA. It sensitively profiles genome-wide off-target cut sites and characterizes the contribution of SNPs to these cleavage events.

See also: News and Views by Urnov

Marker-free coselection for CRISPR-driven genome editing in human cells   pp615 - 620
Daniel Agudelo, Alexis Duringer, Lusiné Bozoyan, Caroline C Huard, Sophie Carter et al.
doi:10.1038/nmeth.4265
A gain-of-function mutation in a sodium/potassium pump renders cells resistant to a small-molecule drug and provides an efficient coselection strategy to enrich for CRISPR-induced mutations at an independent locus.

 

Generation of pure GABAergic neurons by transcription factor programming   pp621 - 628
Nan Yang, Soham Chanda, Samuele Marro, Yi-Han Ng, Justyna A Janas et al.
doi:10.1038/nmeth.4291
Transient transcription factor expression rapidly induces a homogenous population of mature GABAergic neurons from human pluripotent stem cells, aiding the study of inhibitory neuron function and disease.

 

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells   pp629 - 635
Yarui Diao, Rongxin Fang, Bin Li, Zhipeng Meng, Juntao Yu et al.
doi:10.1038/nmeth.4264
CREST-seq allows functional screening of cis-regulatory elements through the use of sgRNA pairs to introduce tiled deletions in regions of interest. The analysis of a 2-megabase target region shows that promoters can act as distal enhancers for unrelated genes.

 
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Application Note

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A humanized phenotypic screening platform for chronic pain   
Daniel Tams, Paul Karila and Ashley Barnes

 
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