Spatial transcriptomics for profiling the tropism of viral vectors in tissues

[1]  Sripriya Ravindra Kumar,et al.  Engineered AAVs for non-invasive gene delivery to rodent and non-human primate nervous systems , 2022, Neuron.

[2]  Miguel R. Chuapoco,et al.  AAV capsid variants with brain-wide transgene expression and decreased liver targeting after intravenous delivery in mouse and marmoset , 2021, Nature Neuroscience.

[3]  Andrew L. Lemire,et al.  EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization , 2021, Cell.

[4]  Evan Z. Macosko,et al.  Peer Review File Manuscript Title: A transcriptomic atlas of mouse cerebellar cortex reveals novel cell types Editorial Notes: Reviewer Comments & Author Rebuttals , 2020 .

[5]  A. Wagers,et al.  Directed evolution of a family of AAV capsid variants enabling potent muscle-directed gene delivery across species , 2021, Cell.

[6]  Gustavo S. França,et al.  Exploring tissue architecture using spatial transcriptomics , 2021, Nature.

[7]  Paul D. Gamlin,et al.  A comprehensive study of a 29 capsid AAV library in non-human primate central nervous system. , 2021, Molecular therapy : the journal of the American Society of Gene Therapy.

[8]  V. Gradinaru,et al.  Deep Parallel Characterization of AAV Tropism and AAV-Mediated Transcriptional Changes via Single-Cell RNA Sequencing , 2021, bioRxiv.

[9]  H. Kang,et al.  Microscopic examination of spatial transcriptome using Seq-Scope , 2021, Cell.

[10]  M. Carlén,et al.  Spatial Transcriptomics: Molecular Maps of the Mammalian Brain. , 2021, Annual review of neuroscience.

[11]  D. Schaffer,et al.  Adeno-Associated Virus Vector for Central Nervous System Gene Therapy. , 2021, Trends in molecular medicine.

[12]  Stephan Fischer,et al.  Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections , 2021, Nature Neuroscience.

[13]  Garreck H. Lenz,et al.  Enhancer viruses for combinatorial cell-subclass-specific labeling , 2021, Neuron.

[14]  Andrew C. Pawlowski,et al.  Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses , 2021, Nucleic acids research.

[15]  S. Paul,et al.  Rapid evolution of blood-brain-barrier-penetrating AAV capsids by RNA-driven biopanning , 2020, Molecular therapy. Methods & clinical development.

[16]  J. Nakai,et al.  GABAergic neuron-specific whole-brain transduction by AAV-PHP.B incorporated with a new GAD65 promoter , 2020, Molecular brain.

[17]  Andrew C. Payne,et al.  Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems , 2020, Science.

[18]  Kirsten L. Frieda,et al.  Imaging cell lineage with a synthetic digital recording system , 2020, Science.

[19]  Lief E. Fenno,et al.  A Molecular Calcium Integrator Reveals a Striatal Cell Type Driving Aversion , 2020, Cell.

[20]  Mingyao Li,et al.  MicroRNA-mediated inhibition of transgene expression reduces dorsal root ganglion toxicity by AAV vectors in primates , 2020, Science Translational Medicine.

[21]  D. Grimm,et al.  Identification of a myotropic AAV by massively parallel in vivo evaluation of barcoded capsid variants , 2020, Nature Communications.

[22]  E. Nestler,et al.  Viral tools for neuroscience , 2020, Nature Reviews Neuroscience.

[23]  S. Lapan,et al.  In Situ Detection of Adeno-associated Viral Vector Genomes with SABER-FISH , 2020, Molecular therapy. Methods & clinical development.

[24]  Sergio Marco Salas,et al.  Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue , 2020, Nucleic acids research.

[25]  S. Quake,et al.  A mouse tissue atlas of small noncoding RNA , 2020, Proceedings of the National Academy of Sciences.

[26]  Tom P. Franken,et al.  Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans , 2020, Nature Neuroscience.

[27]  D. Duan,et al.  High-Resolution Histological Landscape of AAV DNA Distribution in Cellular Compartments and Tissues following Local and Systemic Injection , 2020, Molecular therapy. Methods & clinical development.

[28]  Sripriya Ravindra Kumar,et al.  Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types , 2020, Nature Methods.

[29]  C. Kentros,et al.  Enhancer-Driven Gene Expression (EDGE) Enables the Generation of Viral Vectors Specific to Neuronal Subtypes , 2020, iScience.

[30]  Marius Pachitariu,et al.  Cellpose: a generalist algorithm for cellular segmentation , 2020, Nature Methods.

[31]  G. Wang,et al.  A systematic capsid evolution approach performed in vivo for the design of AAV vectors with tailored properties and tropism , 2019, Proceedings of the National Academy of Sciences.

[32]  Mark W. Budde,et al.  In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription , 2019, Nature Biotechnology.

[33]  E. Hudry,et al.  Selection of an Efficient AAV Vector for Robust CNS Transgene Expression , 2019, Molecular therapy. Methods & clinical development.

[34]  Jonathan L. Schmid-Burgk,et al.  Optical Pooled Screens in Human Cells , 2019, Cell.

[35]  James W. Phillips,et al.  A repeated molecular architecture across thalamic pathways , 2019, Nature Neuroscience.

[36]  Ali H. Cetin,et al.  Adeno-Associated Virus Technologies and Methods for Targeted Neuronal Manipulation , 2019, bioRxiv.

[37]  Xiaodong Li,et al.  MicroRNA-126-3p Attenuates Intracerebral Hemorrhage-Induced Blood-Brain Barrier Disruption by Regulating VCAM-1 Expression , 2019, Front. Neurosci..

[38]  Peng Yin,et al.  SABER enables amplified and multiplexed imaging of RNA and DNA in cells and tissues , 2019, Nature Methods.

[39]  Guo-Cheng Yuan,et al.  Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+ , 2019, Nature.

[40]  Attila Losonczy,et al.  Functional Access to Neuron Subclasses in Rodent and Primate Forebrain , 2019, Cell reports.

[41]  Evan Z. Macosko,et al.  Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution , 2019, Science.

[42]  M. Mortrud,et al.  Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex , 2019, bioRxiv.

[43]  G. Gao,et al.  Adeno-associated virus vector as a platform for gene therapy delivery , 2019, Nature Reviews Drug Discovery.

[44]  Sripriya Ravindra Kumar,et al.  Systemic AAV vectors for widespread and targeted gene delivery in rodents , 2019, Nature Protocols.

[45]  Allan R. Jones,et al.  Shared and distinct transcriptomic cell types across neocortical areas , 2018, Nature.

[46]  Lars E. Borm,et al.  Spatial organization of the somatosensory cortex revealed by osmFISH , 2018, Nature Methods.

[47]  William E. Allen,et al.  Three-dimensional intact-tissue sequencing of single-cell transcriptional states , 2018, Science.

[48]  Viviana Gradinaru,et al.  Viral Strategies for Targeting the Central and Peripheral Nervous Systems. , 2018, Annual review of neuroscience.

[49]  H. Gritton,et al.  A MicroRNA-Based Gene-Targeting Tool for Virally Labeling Interneurons in the Rodent Cortex. , 2018, Cell reports.

[50]  A. Nimmerjahn,et al.  Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors , 2018, Science.

[51]  Johannes Stegmaier,et al.  Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust , 2018, Development.

[52]  H. Maegawa,et al.  Gene Therapy for Neuropathic Pain through siRNA-IRF5 Gene Delivery with Homing Peptides to Microglia , 2018, Molecular therapy. Nucleic acids.

[53]  Mikhail G. Shapiro,et al.  In Vivo Selection of a Computationally Designed SCHEMA AAV Library Yields a Novel Variant for Infection of Adult Neural Stem Cells in the SVZ. , 2018, Molecular therapy : the journal of the American Society of Gene Therapy.

[54]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[55]  George Emanuel,et al.  High-Throughput Image-Based Screening of Pooled Genetic Variant Libraries , 2019 .

[56]  H. Hirai,et al.  Minimal Purkinje Cell-Specific PCP2/L7 Promoter Virally Available for Rodents and Non-human Primates , 2017, Molecular therapy. Methods & clinical development.

[57]  V. Gradinaru,et al.  Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems , 2017, Nature Neuroscience.

[58]  L. Cai,et al.  In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus , 2016, Neuron.

[59]  L. Looger,et al.  A Designer AAV Variant Permits Efficient Retrograde Access to Projection Neurons , 2016, Neuron.

[60]  D. Fitzpatrick,et al.  Opportunities and challenges in modeling human brain disorders in transgenic primates , 2016, Nature Neuroscience.

[61]  Hazen P Babcock,et al.  High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization , 2016, Proceedings of the National Academy of Sciences.

[62]  Stephen R Quake,et al.  Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq. , 2016, Cell reports.

[63]  Edward S Boyden,et al.  Nanoscale Imaging of RNA with Expansion Microscopy , 2016, Nature Methods.

[64]  Christof Koch,et al.  Adult Mouse Cortical Cell Taxonomy by Single Cell Transcriptomics , 2016, Nature Neuroscience.

[65]  Sripriya Ravindra Kumar,et al.  Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain , 2015, Nature Biotechnology.

[66]  X. Zhuang,et al.  Spatially resolved, highly multiplexed RNA profiling in single cells , 2015, Science.

[67]  Kun Zhang,et al.  Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues , 2015, Nature Protocols.

[68]  Charless C. Fowlkes,et al.  Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping , 2015, Nature Protocols.

[69]  Rajan P Kulkarni,et al.  Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing , 2014, Cell.

[70]  Timur Zhiyentayev,et al.  Single-cell in situ RNA profiling by sequential hybridization , 2014, Nature Methods.

[71]  George M. Church,et al.  Highly Multiplexed Subcellular RNA Sequencing in Situ , 2014, Science.

[72]  Jun-Hyeok Choi,et al.  Optimization of AAV expression cassettes to improve packaging capacity and transgene expression in neurons , 2014, Molecular Brain.

[73]  Steven J. M. Jones,et al.  Targeted CNS delivery using human MiniPromoters and demonstrated compatibility with adeno-associated viral vectors , 2014, Molecular therapy. Methods & clinical development.

[74]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[75]  Michael Q. Zhang,et al.  Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain , 2012, Neuron.

[76]  Stefan L Ameres,et al.  MicroRNA-regulated, Systemically Delivered rAAV9: A Step Closer to CNS-restricted Transgene Expression , 2010, Molecular therapy : the journal of the American Society of Gene Therapy.

[77]  Juan Li,et al.  Liver-specific microRNA-122 target sequences incorporated in AAV vectors efficiently inhibits transgene expression in the liver , 2010, Gene Therapy.

[78]  Ola Söderberg,et al.  In situ detection and genotyping of individual mRNA molecules , 2010, Nature Methods.

[79]  K. Obata,et al.  Preferential labeling of inhibitory and excitatory cortical neurons by endogenous tropism of adeno-associated virus and lentivirus vectors , 2009, Neuroscience.

[80]  M. Zavolan,et al.  miRNA in situ hybridization in mammalian tissues fixed with formaldehyde and EDC , 2009, Nature methods.

[81]  Scott A. Rifkin,et al.  Imaging individual mRNA molecules using multiple singly labeled probes , 2008, Nature Methods.

[82]  T. Terwilliger,et al.  Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein , 2005, Nature Biotechnology.