Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

(2020) Michaela Asp et al.   BIOESSAYS

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

(2020) Carly G.K. Ziegler et al.   CELL

Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma

(2020) Lindsay M. LaFave et al.   CANCER CELL

Emergence of a High-Plasticity Cell State during Lung Cancer Evolution

(2020) Nemanja Despot Marjanovic et al.   CANCER CELL

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies

(2020) Travis K. Hughes et al.   IMMUNITY

Establishment of patient-derived cancer organoids for drug-screening applications

(2020) Else Driehuis et al.   Nature Protocols

From whole-mount to single-cell spatial assessment of gene expression in 3D

(2020) Lisa N. Waylen et al.   Communications Biology

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Expansion of human primary hepatocytes in vitro through their amplification as liver progenitors in a 3D organoid system

(2018) Delphine Garnier et al.   Scientific Reports

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis

(2018) Andreas E. Moor et al.   CELL

Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition

(2018) Masayuki Fujii et al.   Cell Stem Cell

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

(2017) Chiara Medaglia et al.   SCIENCE

Ca2+ ionophores are not suitable for inducing mPTP opening in murine isolated adult cardiac myocytes

(2017) Mathieu Panel et al.   Scientific Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Engineering Stem Cell Organoids

(2016) Xiaolei Yin et al.   Cell Stem Cell

Bright photoactivatable fluorophores for single-molecule imaging

(2016) Jonathan B Grimm et al.   NATURE METHODS

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

A smart local moving algorithm for large-scale modularity-based community detection

(2013) Ludo Waltman et al.   EUROPEAN PHYSICAL JOURNAL B

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

(2012) Andrew McDavid et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Molecular Probes handbook. A guide to fluorescent probes and labeling technologies

(2011) G. Ya. Wiederschain   BIOCHEMISTRY-MOSCOW

Intestinal development and differentiation

(2011) Taeko K. Noah et al.   EXPERIMENTAL CELL RESEARCH

Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett's Epithelium

(2011) Toshiro Sato et al.   GASTROENTEROLOGY

Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues

(2010) Dmitriy M. Chudakov et al.   PHYSIOLOGICAL REVIEWS

Wnt Signaling, Lgr5, and Stem Cells in the Intestine and Skin

(2009) Andrea Haegebarth et al.   AMERICAN JOURNAL OF PATHOLOGY

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Conditional mouse lung cancer models using adenoviral or lentiviral delivery of Cre recombinase

(2009) Michel DuPage et al.   Nature Protocols

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Monitoring cellular movement in vivo with photoconvertible fluorescence protein "Kaede" transgenic mice

(2008) M. Tomura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA