Highly multiplexed subcellular RNA sequencing in situ.

PubWeight™: 3.77‹?› | Rank: Top 1%

🔗 View Article (PMC 4140943)

Published in Science on February 27, 2014

Authors

Je Hyuk Lee1, Evan R Daugharthy, Jonathan Scheiman, Reza Kalhor, Joyce L Yang, Thomas C Ferrante, Richard Terry, Sauveur S F Jeanty, Chao Li, Ryoji Amamoto, Derek T Peters, Brian M Turczyk, Adam H Marblestone, Samuel A Inverso, Amy Bernard, Prashant Mali, Xavier Rios, John Aach, George M Church

Author Affiliations

1: Wyss Institute, Harvard Medical School, Boston, MA 02115, USA.

Articles citing this

(truncated to the top 100)

Optical imaging. Expansion microscopy. Science (2015) 3.15

Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling. Science (2014) 2.78

Spatial reconstruction of single-cell gene expression data. Nat Biotechnol (2015) 2.31

Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res (2014) 2.06

Remote control of gene function by local translation. Cell (2014) 1.72

In the right place at the right time: visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol (2014) 1.72

Single-cell genome sequencing: current state of the science. Nat Rev Genet (2016) 1.62

Adult Mammalian Neural Stem Cells and Neurogenesis: Five Decades Later. Cell Stem Cell (2015) 1.54

Toward understanding and exploiting tumor heterogeneity. Nat Med (2015) 1.51

Advances in fluorescence labeling strategies for dynamic cellular imaging. Nat Chem Biol (2014) 1.47

WNK1 kinase balances T cell adhesion versus migration in vivo. Nat Immunol (2016) 1.39

Nature Biotechnology's academic spinouts of 2016. Nat Biotechnol (2017) 1.38

The first five years of single-cell cancer genomics and beyond. Genome Res (2015) 1.27

Defining cell types and states with single-cell genomics. Genome Res (2015) 1.27

Regulation of macrophage development and function in peripheral tissues. Nat Rev Immunol (2015) 1.16

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc (2015) 1.12

Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science (2016) 1.06

Rapid neurogenesis through transcriptional activation in human stem cells. Mol Syst Biol (2014) 1.05

Single-Cell Analysis in Cancer Genomics. Trends Genet (2015) 1.05

Chromatin Domains: The Unit of Chromosome Organization. Mol Cell (2016) 1.02

Scalable microfluidics for single-cell RNA printing and sequencing. Genome Biol (2015) 1.02

Open access to large scale datasets is needed to translate knowledge of cancer heterogeneity into better patient outcomes. PLoS Med (2015) 1.01

Stochastic electrotransport selectively enhances the transport of highly electromobile molecules. Proc Natl Acad Sci U S A (2015) 1.00

Revealing the vectors of cellular identity with single-cell genomics. Nat Biotechnol (2016) 0.97

Nanoscale imaging of RNA with expansion microscopy. Nat Methods (2016) 0.96

In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer. Nat Genet (2015) 0.95

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution. Cell (2016) 0.93

Application of single-cell genomics in cancer: promise and challenges. Hum Mol Genet (2015) 0.90

Scaling single-cell genomics from phenomenology to mechanism. Nature (2017) 0.89

Single-cell transcriptome sequencing: recent advances and remaining challenges. F1000Res (2016) 0.88

Single-cell genome-wide studies give new insight into nongenetic cell-to-cell variability in animals. Histochem Cell Biol (2016) 0.88

Processing, visualising and reconstructing network models from single-cell data. Immunol Cell Biol (2015) 0.88

Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators. Cell Stem Cell (2016) 0.88

Imaging Transcription: Past, Present, and Future. Cold Spring Harb Symp Quant Biol (2016) 0.87

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Cell Syst (2016) 0.86

Single Cell Analysis: From Technology to Biology and Medicine. Single Cell Biol (2014) 0.86

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proc Natl Acad Sci U S A (2016) 0.86

Imaging Specific Genomic DNA in Living Cells. Annu Rev Biophys (2016) 0.86

Single-cell sequencing in stem cell biology. Genome Biol (2016) 0.85

Common variation in atrial fibrillation: navigating the path from genetic association to mechanism. Cardiovasc Res (2016) 0.85

The niche in single-cell technologies. Immunol Cell Biol (2015) 0.85

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus. Neuron (2016) 0.84

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer. Genome Biol (2015) 0.84

Building a lineage from single cells: genetic techniques for cell lineage tracking. Nat Rev Genet (2017) 0.83

Understanding Spatial Genome Organization: Methods and Insights. Genomics Proteomics Bioinformatics (2016) 0.82

RNA-Seq reveals novel transcriptional reorganization in human alcoholic brain. Int Rev Neurobiol (2014) 0.82

Microfluidic Sample Preparation for Single Cell Analysis. Anal Chem (2015) 0.82

The promises and challenges of human brain organoids as models of neuropsychiatric disease. Nat Med (2016) 0.81

A Bead-Based Microfluidic Approach to Integrated Single-Cell Gene Expression Analysis by Quantitative RT-PCR. RSC Adv (2015) 0.81

A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate. Development (2015) 0.81

Strength in numbers: quantitative single-molecule RNA detection assays. Wiley Interdiscip Rev Dev Biol (2015) 0.81

The female gametophyte: an emerging model for cell type-specific systems biology in plant development. Front Plant Sci (2015) 0.81

Obstacles and opportunities in the functional analysis of extracellular vesicle RNA - an ISEV position paper. J Extracell Vesicles (2017) 0.80

Variation is function: Are single cell differences functionally important?: Testing the hypothesis that single cell variation is required for aggregate function. Bioessays (2015) 0.80

RNA sequencing in situ. Nat Biotechnol (2014) 0.80

Unexpected targets and triggers of autoimmunity. J Clin Immunol (2014) 0.80

Redefining Signaling Pathways with an Expanding Single-Cell Toolbox. Trends Biotechnol (2016) 0.80

Programmable RNA-binding protein composed of repeats of a single modular unit. Proc Natl Acad Sci U S A (2016) 0.80

Single cell transcriptomics: methods and applications. Front Oncol (2015) 0.80

The promise of organ and tissue preservation to transform medicine. Nat Biotechnol (2017) 0.80

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing. Proc Natl Acad Sci U S A (2016) 0.79

Dense transcript profiling in single cells by image correlation decoding. Nat Methods (2016) 0.79

Puzzle Imaging: Using Large-Scale Dimensionality Reduction Algorithms for Localization. PLoS One (2015) 0.79

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq. Genome Biol (2014) 0.78

Proteostasis and RNA Binding Proteins in Synaptic Plasticity and in the Pathogenesis of Neuropsychiatric Disorders. Neural Plast (2016) 0.78

What to compare and how: Comparative transcriptomics for Evo-Devo. J Exp Zool B Mol Dev Evol (2015) 0.78

Rapidly evolving homing CRISPR barcodes. Nat Methods (2016) 0.78

Challenges and emerging directions in single-cell analysis. Genome Biol (2017) 0.77

An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries. Sci Rep (2016) 0.77

The organization and regulation of mRNA-protein complexes. Wiley Interdiscip Rev RNA (2016) 0.77

Iterative expansion microscopy. Nat Methods (2017) 0.77

Rolling circle replication requires single-stranded DNA binding protein to avoid termination and production of double-stranded DNA. Nucleic Acids Res (2014) 0.77

The Emerging Function and Mechanism of ceRNAs in Cancer. Trends Genet (2016) 0.77

Gene expression profiling in the human alcoholic brain. Neuropharmacology (2017) 0.76

3D computational reconstruction of tissues with hollow spherical morphologies using single-cell gene expression data. Nat Protoc (2015) 0.76

Multiscale analysis of the murine intestine for modeling human diseases. Integr Biol (Camb) (2015) 0.76

Seeing is believing: new methods for in situ single-cell transcriptomics. Genome Biol (2014) 0.76

Computational Tools for Stem Cell Biology. Trends Biotechnol (2016) 0.76

4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation? Genome Biol (2016) 0.76

Single-Cell and Single-Molecule Analysis of Gene Expression Regulation. Annu Rev Genet (2016) 0.76

Genomic analysis of RNA localization. RNA Biol (2014) 0.76

Internalization and observation of fluorescent biomolecules in living microorganisms via electroporation. J Vis Exp (2015) 0.76

Fourth-generation sequencing in the cell and the clinic. Genome Med (2014) 0.76

Systems Biology Approaches for Host-Fungal Interactions: An Expanding Multi-Omics Frontier. OMICS (2016) 0.76

A retrograde adeno-associated virus for collecting ribosome-bound mRNA from anatomically defined projection neurons. Front Mol Neurosci (2015) 0.76

Quantitative approaches for investigating the spatial context of gene expression. Wiley Interdiscip Rev Syst Biol Med (2016) 0.75

Progress in the clinical detection of heterogeneity in breast cancer. Cancer Med (2016) 0.75

Fourth Generation of Next-Generation Sequencing Technologies: Promise and Consequences. Hum Mutat (2016) 0.75

What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. Mol Cell (2016) 0.75

Platform for combined analysis of functional and biomolecular phenotypes of the same cell. Sci Rep (2017) 0.75

Identification of clinically predictive metagenes that encode components of a network coupling cell shape to transcription by image-omics. Genome Res (2016) 0.75

Single-cell states versus single-cell atlases - two classes of heterogeneity that differ in meaning and method. Curr Opin Biotechnol (2016) 0.75

HDTD: analyzing multi-tissue gene expression data. Bioinformatics (2016) 0.75

Assessing characteristics of RNA amplification methods for single cell RNA sequencing. BMC Genomics (2016) 0.75

Extensible Multiplex Real-time PCR of MicroRNA Using Microparticles. Sci Rep (2016) 0.75

Single Cell Isolation and Analysis. Front Cell Dev Biol (2016) 0.75

Cerebral cortical neuron diversity and development at single-cell resolution. Curr Opin Neurobiol (2016) 0.75

The Development and Analysis of Integrated Neuroscience Data. Front Comput Neurosci (2016) 0.75

The big RNA picture. Nat Methods (2014) 0.75

Omics approaches to individual variation: modeling networks and the virtual patient. Dialogues Clin Neurosci (2016) 0.75

Articles cited by this

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99

Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci U S A (1988) 35.13

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (2009) 21.24

Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91

Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature (2007) 12.76

Visualization of single RNA transcripts in situ. Science (1998) 10.51

Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods (2008) 10.40

Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell (2007) 8.43

Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science (2007) 5.19

Single-cell gene expression profiling. Science (2002) 5.07

A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol (2011) 4.84

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods (2009) 4.38

A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet (2009) 2.78

Digital genotyping and haplotyping with polymerase colonies. Proc Natl Acad Sci U S A (2003) 2.77

Large-scale cellular-resolution gene profiling in human neocortex reveals species-specific molecular signatures. Cell (2012) 2.29

Validating transcripts with probes and imaging technology. Nat Methods (2011) 2.15

In situ sequencing for RNA analysis in preserved tissue and cells. Nat Methods (2013) 2.13

Fibroblasts and myofibroblasts: their source, function and role in disease. Int J Biochem Cell Biol (2006) 2.02

The fibronectin gene as a model for splicing and transcription studies. FASEB J (1996) 1.81

Articles by these authors

RNA-guided human genome engineering via Cas9. Science (2013) 48.29

Genome-wide atlas of gene expression in the adult mouse brain. Nature (2006) 28.02

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (2009) 21.24

Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91

Multiplex amplification of large sets of human exons. Nat Methods (2007) 15.11

Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29

Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol (2011) 12.86

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol (2013) 11.35

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol (2009) 11.18

Clinical assessment incorporating a personal genome. Lancet (2010) 10.18

Advanced sequencing technologies: methods and goals. Nat Rev Genet (2004) 9.31

Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell (2009) 8.97

Modular epistasis in yeast metabolism. Nat Genet (2004) 8.64

Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A (2002) 8.41

Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol (2005) 8.32

Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A (2003) 7.95

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res (2013) 7.77

Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol (2006) 7.64

Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science (2009) 6.96

A highly annotated whole-genome sequence of a Korean individual. Nature (2009) 6.91

Cas9 as a versatile tool for engineering biology. Nat Methods (2013) 6.87

From genetic privacy to open consent. Nat Rev Genet (2008) 5.95

Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods (2013) 5.93

The brain activity map project and the challenge of functional connectomics. Neuron (2012) 5.52

Computational and experimental identification of C. elegans microRNAs. Mol Cell (2003) 5.22

Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science (2007) 5.19

A logic-gated nanorobot for targeted transport of molecular payloads. Science (2012) 4.96

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 4.83

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods (2013) 4.61

Genome engineering. Nat Biotechnol (2009) 4.60

Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell (2006) 4.51

A TALEN genome-editing system for generating human stem cell-based disease models. Cell Stem Cell (2012) 4.49

Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci U S A (2002) 4.44

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods (2009) 4.38

Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet (2007) 4.25

Human-induced pluripotent stem cells from blood cells of healthy donors and patients with acquired blood disorders. Blood (2009) 4.22

Tuberculosis drug resistance mutation database. PLoS Med (2009) 4.13

Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol (2002) 4.00

Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol (2013) 3.84

Quantitative morphological signatures define local signaling networks regulating cell morphology. Science (2007) 3.76

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature (2012) 3.74

A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A (2012) 3.72

Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A (2006) 3.68

A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol (2006) 3.68

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell (2011) 3.61

Efficient human iPS cell derivation by a non-integrating plasmid from blood cells with unique epigenetic and gene expression signatures. Cell Res (2011) 3.58

Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics (2009) 3.50

Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science (2011) 3.49

Bacteria subsisting on antibiotics. Science (2008) 3.47

Site-specific gene correction of a point mutation in human iPS cells derived from an adult patient with sickle cell disease. Blood (2011) 3.43

Information access. Raw personal data: providing access. Science (2014) 3.41

Neuroscience. The brain activity map. Science (2013) 3.36

Generation of functional human hepatic endoderm from human induced pluripotent stem cells. Hepatology (2010) 3.36

The complete genome and proteome of Mycoplasma mobile. Genome Res (2004) 3.36

Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol (2002) 3.28

Gene synthesis by circular assembly amplification. Nat Methods (2007) 3.21

Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet (2011) 3.20

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol (2010) 3.14

Photosynthesis genes in marine viruses yield proteins during host infection. Nature (2005) 2.99

The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell (2006) 2.99

Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res (2003) 2.97

Reprogramming of T cells from human peripheral blood. Cell Stem Cell (2010) 2.93

Automated modelling of signal transduction networks. BMC Bioinformatics (2002) 2.92

Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res (2009) 2.91

The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop. Genet Med (2009) 2.91

The challenges of sequencing by synthesis. Nat Biotechnol (2009) 2.89

A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet (2009) 2.78

Optimization of scarless human stem cell genome editing. Nucleic Acids Res (2013) 2.78

Digital genotyping and haplotyping with polymerase colonies. Proc Natl Acad Sci U S A (2003) 2.77

Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics (2004) 2.76

Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res (2002) 2.74

Nanotools for neuroscience and brain activity mapping. ACS Nano (2013) 2.74

Genomically recoded organisms expand biological functions. Science (2013) 2.73

Fluorescent in situ sequencing on polymerase colonies. Anal Biochem (2003) 2.70

High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol (2010) 2.68

The amino-acid mutational spectrum of human genetic disease. Genome Biol (2003) 2.55

Towards synthesis of a minimal cell. Mol Syst Biol (2006) 2.55

Prehabilitation versus rehabilitation: a randomized control trial in patients undergoing colorectal resection for cancer. Anesthesiology (2014) 2.53

Identification of foreign gene sequences by transcript filtering against the human genome. Nat Genet (2002) 2.52

Regulatory network of acid resistance genes in Escherichia coli. Mol Microbiol (2003) 2.42

Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res (2009) 2.38

Genomic anatomy of the hippocampus. Neuron (2008) 2.37