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TABLE OF CONTENTS |
June 2017 Volume 14, Issue 6 |
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| In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Perspective Brief Communications Articles Application Note
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nature.com webcasts Join us for our upcoming webcast followed by live Q&A: MAKING A NAME IN CANCER IMMUNOTHERAPY Presented by BioPharma Dealmakers Date: Tuesday, 13 June, 2017 Time: 8AM PDT | 11AM EDT | 4PM BST | 5PM CEST REGISTER FOR FREE Sponsored by: Immunomic Therapeutics, Inc., | IsoPlexis | Merus N.V. | Actinium Pharmaceuticals, Inc. | | | |
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In This Issue | Top |
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In This Issue |
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Editorial | Top |
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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.
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This Month | Top |
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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.
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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.
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Correspondence | Top |
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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
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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
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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
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Research Highlights | Top |
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Technology Feature | Top |
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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.
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News and Views | Top |
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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. |
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Perspective | Top |
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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.
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Brief Communications | Top |
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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.
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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.
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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.
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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.
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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.
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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 |
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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.
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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 |
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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 |
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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.
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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.
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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 | Top |
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A humanized phenotypic screening platform for chronic pain Daniel Tams, Paul Karila and Ashley Barnes
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