Volume 14 Issue 6, June 2017

Teamwork on and off the ice, and tipping the odds to find CRISPR hits sans markers.

Clustering finds patterns in data—whether they are there or not.

A proximity labeling technique yields new insights into GPCR signaling.

Researchers optimize stimulated Raman scattering microscopy and combine it with a new panel of Raman-active dyes to enable 24-color bioimaging.

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

A chemical combination enables culture of pluripotent cells.

A multicolor reporter mouse model enables monitoring of the fate and dynamics of microglia in health and disease.

3D human cell cultures are changing the way scientists model organ development and function—but they have their own set of complications.

Useful new methods are being introduced to experimentally determine the genome-wide consequences of Cas9-based editing.

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.

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.

CRISPR interference screens with pairs of sgRNAs allow for quantitative characterization of genetic interactions.

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 normalizes single-cell RNA-seq data for improved downstream analyses such as differential expression and cell-state discrimination.

ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates.

HipSTR accurately genotypes and phases short tandem repeats, enabling robust genome-wide analyses of short tandem repeat variations.

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.

SITE-Seq probes Cas9 cleavage sites in vitro and returns a comprehensive list of off-target sites at different Cas9–sgRNA concentrations.

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.

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.

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.

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.