Brief Communication |
Featured
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Brief Communication |
Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells
DART-seq alters droplet sequencing in a simple and flexible way to simultaneously profile the transcriptome and multiplexed targeted RNAs, such as viral transcripts and immunoglobulin chains, in single cells.
- Mridusmita Saikia
- , Philip Burnham
- & Iwijn De Vlaminck
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Brief Communication |
Spatial organization of the somatosensory cortex revealed by osmFISH
osmFISH applies automated cycles of single-molecule fluorescence in situ hybridization without barcoding to provide spatial gene expression in tissue sections at high sensitivity, accuracy and throughput.
- Simone Codeluppi
- , Lars E. Borm
- & Sten Linnarsson
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Article |
Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms
TECtool identifies terminal exons from RNA-seq data, uncovering novel isoforms, many of which are translated.
- Andreas J. Gruber
- , Foivos Gypas
- & Mihaela Zavolan
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Research Highlight |
Transcript constellations in a tissue’s universe
The STARmap method advances RNA sequencing in intact tissues.
- Tal Nawy
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Research Highlight |
Transcripts from a spliceosome
Two new methods provide high-resolution profiles of splicing events in yeast.
- Tal Nawy
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Analysis |
Comprehensive comparative analysis of 5′-end RNA-sequencing methods
A direct comparison of 5′-end RNA-seq methods reveals strong performance by CAGE, and identifies differential transcriptional start site usage among brain-related samples.
- Xian Adiconis
- , Adam L. Haber
- & Joshua Z. Levin
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Technology Feature |
Stem cells: lineage tracing lets single cells talk about their past
Multipotent stem cells can become a variety of cell types. A flurry of new approaches enable lineage tracing at single-cell resolution.
- Vivien Marx
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Methods in Brief |
Single-cell hat trick
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Brief Communication |
SpatialDE: identification of spatially variable genes
SpatialDE identifies genes with significant spatial expression patterns from multiplexed imaging or spatial RNA-sequencing data, and can cluster genes with similar spatial patterns as a form of expression-based tissue histology.
- Valentine Svensson
- , Sarah A Teichmann
- & Oliver Stegle
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Research Highlights |
Transcriptomics in the NICHE
The combination of photoactivatable fluorescent markers with single-cell RNA-seq allows transcriptome analysis of cells from specific tissue locations.
- Irene Jarchum
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Brief Communication |
On the design of CRISPR-based single-cell molecular screens
CRISPR-based single-cell pooled screens that use linked barcodes suffer from lost sensitivity due to lentiviral template switching. The barcode-free CROP-seq design circumvents this problem.
- Andrew J Hill
- , José L McFaline-Figueroa
- & Cole Trapnell
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Technology Feature |
Neurobiology: gene expression captured on-site
A wealth of spatial techniques capture the 'where' of gene expression.
- Vivien Marx
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Brief Communication |
SCENIC: single-cell regulatory network inference and clustering
SCENIC enables simultaneous regulatory network inference and robust cell clustering from single-cell RNA-seq data.
- Sara Aibar
- , Carmen Bravo González-Blas
- & Stein Aerts
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Brief Communication |
Reversed graph embedding resolves complex single-cell trajectories
Monocle 2 uses reversed graph embedding to automatically learn complex, branched pseudotime trajectories of differentiation or cellular state changes from single-cell expression data.
Monocle 2 uses reversed graph embedding to automatically learn complex, branched pseudotime trajectories of differentiation or cellular state changes from single-cell expression data.
- Xiaojie Qiu
- , Qi Mao
- & Cole Trapnell
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Brief Communication |
Simultaneous epitope and transcriptome measurement in single cells
Using established high-throughput single-cell RNA-seq platforms, CITE-seq combines highly multiplexed, antibody-based protein marker quantification with unbiased transcriptome profiling for thousands of single cells.
- Marlon Stoeckius
- , Christoph Hafemeister
- & Peter Smibert
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Research Highlights |
Organoid variability examined
Single-cell transcriptomics is used to determine what cell types are present in brain organoids and how much these cell types vary across organoids.
- Natalie de Souza
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Tools in Brief |
One mouse to trap them all
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Technology Feature |
Choosing CRISPR-based screens in cancer
Many possibilities for parsing cancer emerge when labs combine gene editing and screens. And RNAi retains its spot in the menu of options.
- Vivien Marx
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Brief Communication |
Salmon provides fast and bias-aware quantification of transcript expression
Salmon is a computational tool that uses sample-specific models and a dual-phase inference procedure to correct biases in RNA-seq data and rapidly quantify transcript abundances.
- Rob Patro
- , Geet Duggal
- & Carl Kingsford
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Analysis |
Power analysis of single-cell RNA-sequencing experiments
A comparison framework applied to 15 single-cell RNA-seq protocols reveals differences in accuracy and sensitivity and discusses the utility of RNA spike-in standards.
- Valentine Svensson
- , Kedar Nath Natarajan
- & Sarah A Teichmann
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Article |
Pooled CRISPR screening with single-cell transcriptome readout
CROP-seq enables pooled CRISPR screens for complex transcriptome signatures by making gRNA expression detectable in single-cell RNA sequencing.
- Paul Datlinger
- , André F Rendeiro
- & Christoph Bock
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This Month |
Tim R. Mercer
Sequins can help labs see how well a sequencing experiment is going. Surfing experiments are another matter.
- Vivien Marx
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Article |
Spliced synthetic genes as internal controls in RNA sequencing experiments
Synthetic spike-in standards (‘sequins’), representing spliced mRNA isoforms, provide internal controls for assessing transcript assembly and quantification within and between RNA sequencing libraries. Sequins representing fused genes can be used to determine the sensitivity limit for oncogenic fusions in cancer samples.
- Simon A Hardwick
- , Wendy Y Chen
- & Tim R Mercer
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Article |
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
Enhanced CLIP yields complex libraries of RNA components of ribonucleoprotein complexes and maintains single-nucleotide resolution of binding sites. eCLIP enables large scale profiling, as demonstrated with the binding profiles of 73 RBPs in two human cancer cell lines.
- Eric L Van Nostrand
- , Gabriel A Pratt
- & Gene W Yeo
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Brief Communication |
Inntags: small self-structured epitopes for innocuous protein tagging
A set of small, innocuous protein tags, named inntags, show advantages over commonly used epitope tags in a variety of biological applications.
- Maya V Georgieva
- , Galal Yahya
- & Martí Aldea
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Brief Communication |
Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments
Oscope enables the detection of oscillating genes and phasing of cell states from snapshot single-cell RNA-seq data.
- Ning Leng
- , Li-Fang Chu
- & Christina Kendziorski
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Methods in Brief |
Thousands of cell droplets
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Research Highlights |
Catching Pol II in the act
Two methods capture the pausing behavior of RNA polymerase II as it generates messages from mammalian genomes.
- Tal Nawy
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Research Highlights |
RNA structure served in vivo
Two transcriptome-scale sequencing methods provide a more complete view of RNA structure in its native context.
- Tal Nawy
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Research Highlights |
Cellular diversity in a snapshot
A new platform detains single cells in picoliter wells to generate transcriptional profiles in large numbers.
- Tal Nawy
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Methods in Brief |
RNA caps in bacteria stabilize transcripts
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Method to Watch |
Understanding noncoding RNAs
Methods to profile and characterize the function of noncoding RNAs will emerge.
- Nicole Rusk
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Research Highlights |
Rereading familiar messages
Two surveys of the transcriptome hint at unexpected diversity in the breadth of mRNA modifications.
- Michael Eisenstein
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Brief Communication |
Bayesian approach to single-cell differential expression analysis
A method to model expression variability in single-cell RNA-seq measurements and thus to improve subsequent data analysis.
- Peter V Kharchenko
- , Lev Silberstein
- & David T Scadden
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Methods in Brief |
Profiling of RNA editing
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Editorial |
Method of the Year 2013
Methods to sequence the DNA and RNA of single cells are poised to transform many areas of biology and medicine.
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Primer |
Single-cell sequencing
A brief overview of how to derive a genome or transcriptome from a single cell.
- Tal Nawy
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Commentary |
The promise of single-cell sequencing
Individual cells of the same phenotype are commonly viewed as identical functional units of a tissue or organ. However, the deep sequencing of DNA and RNA from single cells suggests a more complex ecology of heterogeneous cell states that together produce emergent system-level function. Continuing development of high-content, real-time, multimodal single-cell measurement technologies will lead to the ultimate goal of understanding the function of an individual cell in the context of its microenvironment.
- James Eberwine
- , Jai-Yoon Sul
- & Junhyong Kim
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Commentary |
Entering the era of single-cell transcriptomics in biology and medicine
Recent technical advances have enabled RNA sequencing (RNA-seq) in single cells. Exploratory studies have already led to insights into the dynamics of differentiation, cellular responses to stimulation and the stochastic nature of transcription. We are entering an era of single-cell transcriptomics that holds promise to substantially impact biology and medicine.
- Rickard Sandberg
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News Feature |
Singled out for sequencing
Single-cell genome and transcriptome sequencing methods are generating a fresh wave of biological insights into development, cancer and neuroscience. Kelly Rae Chi reports.
- Kelly Rae Chi
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Brief Communication |
Quantitative single-cell RNA-seq with unique molecular identifiers
With an optimized protocol and unique molecular identifiers (UMIs) to tag individual transcripts, the mRNA complement of a single cell can be quantified on an absolute scale with almost no amplification bias.
- Saiful Islam
- , Amit Zeisel
- & Sten Linnarsson
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Analysis |
Quantitative assessment of single-cell RNA-sequencing methods
A systematic evaluation of various single-cell RNA-seq approaches reports their sensitivity, accuracy and reproducibility and establishes the high performance of a high-throughput microfluidic method.
- Angela R Wu
- , Norma F Neff
- & Stephen R Quake
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Article |
Image-based transcriptomics in thousands of single human cells at single-molecule resolution
An automated experimental and software pipeline for large-scale FISH enables spatial transcriptomics in thousands of single human cells at single-molecule resolution.
- Nico Battich
- , Thomas Stoeger
- & Lucas Pelkmans