SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution
Authors
Keywords
Probe hybridization, Epithelium, Gene expression, Ligases, Trachea, Lung development, RNA sequencing, RNA hybridization
Journal
PLOS BIOLOGY
Volume 18, Issue 11, Pages e3000675
Publisher
Public Library of Science (PLoS)
Online
2020-11-21
DOI
10.1371/journal.pbio.3000675
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution
- (2019) Samuel G. Rodriques et al. SCIENCE
- Lung regeneration by multipotent stem cells residing at the bronchioalveolar-duct junction
- (2019) Qiaozhen Liu et al. NATURE GENETICS
- Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
- (2019) Chee-Huat Linus Eng et al. NATURE
- Single molecule chromogenic in situ hybridization assay for RNA visualization in fixed cells and tissues
- (2019) Meng Jiang et al. RNA
- Comprehensive Integration of Single-Cell Data
- (2019) Tim Stuart et al. CELL
- High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules
- (2019) Salvatore A. E. Marras et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl
- (2019) Juan C. Caicedo et al. NATURE METHODS
- Human lung branching morphogenesis is orchestrated by the spatiotemporal distribution of ACTA2, SOX2, and SOX9
- (2018) Soula Danopoulos et al. AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY
- Ager-CreERT2: A New Genetic Tool for Studying Lung Alveolar Development, Homeostasis, and Repair
- (2018) Mei-I Chung et al. AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
- Myoepithelial Cells of Submucosal Glands Can Function as Reserve Stem Cells to Regenerate Airways after Injury
- (2018) Aleksandra Tata et al. Cell Stem Cell
- Placing RNA in context and space - methods for spatially resolved transcriptomics
- (2018) Carina Strell et al. FEBS Journal
- Three-dimensional intact-tissue sequencing of single-cell transcriptional states
- (2018) Xiao Wang et al. SCIENCE
- Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells
- (2018) Ahmad N. Nabhan et al. SCIENCE
- RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection
- (2018) Hirokazu Takahashi et al. Scientific Reports
- CellProfiler 3.0: Next-generation image processing for biology
- (2018) Claire McQuin et al. PLOS BIOLOGY
- Automated cell-type classification in intact tissues by single-cell molecular profiling
- (2018) Monica Nagendran et al. eLife
- A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte
- (2018) Lindsey W. Plasschaert et al. NATURE
- A revised airway epithelial hierarchy includes CFTR-expressing ionocytes
- (2018) Daniel T. Montoro et al. NATURE
- ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification
- (2018) Sara H Rouhanifard et al. NATURE BIOTECHNOLOGY
- Spatial organization of the somatosensory cortex revealed by osmFISH
- (2018) Simone Codeluppi et al. NATURE METHODS
- Chimeric padlock and iLock probes for increased efficiency of targeted RNA detection
- (2018) Tomasz Krzywkowski et al. RNA
- Preexisting endothelial cells mediate cardiac neovascularization after injury
- (2017) Lingjuan He et al. JOURNAL OF CLINICAL INVESTIGATION
- Comparative Analysis of Single-Cell RNA Sequencing Methods
- (2017) Christoph Ziegenhain et al. MOLECULAR CELL
- Fidelity of RNA templated end-joining by chlorella virus DNA ligase and a novel iLock assay with improved direct RNA detection accuracy
- (2017) Tomasz Krzywkowski et al. NUCLEIC ACIDS RESEARCH
- Transcription factor Etv5 is essential for the maintenance of alveolar type II cells
- (2017) Zhen Zhang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids
- (2017) Marko Z Nikolić et al. eLife
- The Origins and Functions of Tissue-Resident Macrophages in Kidney Development
- (2017) David A. D. Munro et al. Frontiers in Physiology
- Promoter Specificity and Efficacy in Conditional and Inducible Transgenic Targeting of Lung Macrophages
- (2017) Alexandra L. McCubbrey et al. Frontiers in Immunology
- Mapping a multiplexed zoo of mRNA expression
- (2016) Harry M. T. Choi et al. DEVELOPMENT
- Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing
- (2016) Sheel Shah et al. DEVELOPMENT
- In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus
- (2016) Sheel Shah et al. NEURON
- Efficient in situ detection of mRNAs using the Chlorella virus DNA ligase for padlock probe ligation
- (2016) Nils Schneider et al. RNA
- Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
- (2016) P. L. Stahl et al. SCIENCE
- Spatially resolved, highly multiplexed RNA profiling in single cells
- (2015) K. H. Chen et al. SCIENCE
- Progenitor Cells in Proximal Airway Epithelial Development and Regeneration
- (2014) Thomas J. Lynch et al. JOURNAL OF CELLULAR BIOCHEMISTRY
- Comparative analysis of the efficiency and specificity of myeloid-Cre deleting strains using ROSA-EYFP reporter mice
- (2014) Clare L. Abram et al. JOURNAL OF IMMUNOLOGICAL METHODS
- Alveolar progenitor and stem cells in lung development, renewal and cancer
- (2014) Tushar J. Desai et al. NATURE
- Single-cell in situ RNA profiling by sequential hybridization
- (2014) Eric Lubeck et al. NATURE METHODS
- Type 2 alveolar cells are stem cells in adult lung
- (2013) Christina E. Barkauskas et al. JOURNAL OF CLINICAL INVESTIGATION
- In situ sequencing for RNA analysis in preserved tissue and cells
- (2013) Rongqin Ke et al. NATURE METHODS
- Surfactant Protein–C Chromatin-Bound Green Fluorescence Protein Reporter Mice Reveal Heterogeneity of Surfactant Protein C–Expressing Lung Cells
- (2012) Joo-Hyeon Lee et al. AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
- Fiji: an open-source platform for biological-image analysis
- (2012) Johannes Schindelin et al. NATURE METHODS
- Integrin α6β4 identifies an adult distal lung epithelial population with regenerative potential in mice
- (2011) Harold A. Chapman et al. JOURNAL OF CLINICAL INVESTIGATION
- RNAscope
- (2011) Fay Wang et al. JOURNAL OF MOLECULAR DIAGNOSTICS
- Globally optimal stitching of tiled 3D microscopic image acquisitions
- (2009) S. Preibisch et al. BIOINFORMATICS
- The role of hypoxia and neurogenic genes (Mash-1 and Prox-1) in the developmental programming and maturation of pulmonary neuroendocrine cells in fetal mouse lung
- (2009) Suzanne McGovern et al. LABORATORY INVESTIGATION
- A robust and high-throughput Cre reporting and characterization system for the whole mouse brain
- (2009) Linda Madisen et al. NATURE NEUROSCIENCE
- The branching programme of mouse lung development
- (2008) Ross J. Metzger et al. NATURE
- Imaging individual mRNA molecules using multiple singly labeled probes
- (2008) Arjun Raj et al. NATURE METHODS
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationPublish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn More