4.8 Article

Imaging-based screens of pool-synthesized cell libraries

Related references

Note: Only part of the references are listed.
Review Biotechnology & Applied Microbiology

Uncovering an Organ's Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics

Jie Liao et al.

Summary: Spatially resolved transcriptomics techniques provide near-single-cell or even subcellular resolution within tissues, revealing fine-scale cellular heterogeneity and the functional and structural foundations of tissue architecture. Mapping the whole 3D transcriptional landscape of tissues with position-coordinating labels enables massive information across higher dimensions.

TRENDS IN BIOTECHNOLOGY (2021)

Article Cell Biology

High-content imaging-based pooled CRISPR screens in mammalian cells

Xiaowei Yan et al.

Summary: A microscopy-based optical enrichment approach was developed for selecting and marking cells displaying specific CRISPR-induced phenotypes, followed by isolation using fluorescence-activated cell sorting (FAG). Automated phenotypic identification and photoactivation of cells were achieved through a plugin developed for the open source software mu Manager, allowing screening of approximately 1.5 million individual cells in 8 hours. This scalable approach facilitated the identification of 14 bona fide hits out of 6,092 sgRNAs targeting 544 genes in terms of their effects on nuclear size regulation.

JOURNAL OF CELL BIOLOGY (2021)

Article Cell Biology

Image-based pooled whole-genome CRISPRi screening for subcellular phenotypes

Gil Kanfer et al.

Summary: Utilizing machine learning and convolutional neural network models, researchers have developed a new CRISPR screening method that can study a wider range of cellular and subcellular phenotypes. This approach identifies genetically altered phenotypes accurately through AI algorithms and identifies key factors affecting TFEB subcellular localization at a genome-wide level.

JOURNAL OF CELL BIOLOGY (2021)

Article Biotechnology & Applied Microbiology

In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription

Amjad Askary et al.

NATURE BIOTECHNOLOGY (2020)

Article Biochemical Research Methods

Isolating live cells after high-throughput, long-term, time-lapse microscopy

Scott Luro et al.

NATURE METHODS (2020)

Article Biochemical Research Methods

Time-resolved imaging-based CRISPRi screening

Daniel Camsund et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

Coupling delay controls synchronized oscillation in the segmentation clock

Kumiko Yoshioka-Kobayashi et al.

NATURE (2020)

Article Multidisciplinary Sciences

Improved bacterial recombineering by parallelized protein discovery

Timothy M. Wannier et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemical Research Methods

Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors

Emily C. Wheeler et al.

NATURE METHODS (2020)

Review Genetics & Heredity

Lineage tracing meets single-cell omics: opportunities and challenges

Daniel E. Wagner et al.

NATURE REVIEWS GENETICS (2020)

Article Biochemistry & Molecular Biology

High-throughput, microscope-based sorting to dissect cellular heterogeneity

Nicholas Hasle et al.

MOLECULAR SYSTEMS BIOLOGY (2020)

Review Biochemical Research Methods

AI on a chip

Akihiro Isozaki et al.

LAB ON A CHIP (2020)

Article Multidisciplinary Sciences

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

Chee-Huat Linus Eng et al.

NATURE (2019)

Article Genetics & Heredity

Massively Parallel Assays and Quantitative Sequence–Function Relationships

Justin B. Kinney et al.

Annual Review of Genomics and Human Genetics (2019)

Review Biochemical Research Methods

Deep learning for cellular image analysis

Erick Moen et al.

NATURE METHODS (2019)

Article Multidisciplinary Sciences

Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization

Chong Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Massively parallel screening of synthetic microbial communities

Jared Kehe et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Editorial Material Multidisciplinary Sciences

STARFISH ENTERPRISE: RNA GOES SPATIAL

Jeffrey M. Perkel

NATURE (2019)

Article Multidisciplinary Sciences

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

Chenglong Xia et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

Optical Pooled Screens in Human Cells

David Feldman et al.

Article Multidisciplinary Sciences

Search-and-replace genome editing without double-strand breaks or donor DNA

Andrew V. Anzalone et al.

NATURE (2019)

Review Biochemistry & Molecular Biology

Single-Molecule Kinetics in Living Cells

Johan Elf et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 88 (2019)

Article Biochemical Research Methods

Single-cell microscopy of suspension cultures using a microfluidics-assisted cell screening platform

Burak Okumus et al.

NATURE PROTOCOLS (2018)

Review Genetics & Heredity

Am I ready for CRISPR? A user's guide to genetic screens

John G. Doench

NATURE REVIEWS GENETICS (2018)

Article Biochemistry & Molecular Biology

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

Sheel Shah et al.

Review Microbiology

Microfluidics and single-cell microscopy to study stochastic processes in bacteria

Laurent Potvin-Trottier et al.

CURRENT OPINION IN MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

Blastocyst-like structures generated solely from stem cells

Nicolas C. Rivron et al.

NATURE (2018)

Article Biochemistry & Molecular Biology

A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters

Kiryl D. Piatkevich et al.

NATURE CHEMICAL BIOLOGY (2018)

Article Biochemical Research Methods

Metagenomic mining of regulatory elements enables programmable species-selective gene expression

Nathan I. Johns et al.

NATURE METHODS (2018)

Article Multidisciplinary Sciences

Combinatorial drug discovery in nanoliter droplets

Anthony Kulesa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

Ghost cytometry

Sadao Ota et al.

SCIENCE (2018)

Article Biochemistry & Molecular Biology

CellProfiler 3.0: Next-generation image processing for biology

Claire McQuin et al.

PLOS BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing

Eilon Sharon et al.

Article Biochemistry & Molecular Biology

Intelligent Image-Activated Cell Sorting

Nao Nitta et al.

Article Multidisciplinary Sciences

High-throughput chromatin accessibility profiling at single-cell resolution

Anja Mezger et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

In situ genotyping of a pooled strain library after characterizing complex phenotypes

Michael J. Lawson et al.

MOLECULAR SYSTEMS BIOLOGY (2017)

Article Biochemical Research Methods

High-throughput, image-based screening of pooled genetic-variant libraries

George Emanuel et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Pooled CRISPR screening with single-cell transcriptome readout

Paul Datlinger et al.

NATURE METHODS (2017)

Article Multidisciplinary Sciences

Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging

Ozden Baltekin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Biochemistry & Molecular Biology

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

Jason M. Peters et al.

Article Biochemistry & Molecular Biology

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

Diego Adhemar Jaitin et al.

Article Biochemical Research Methods

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

Mark-Anthony Bray et al.

NATURE PROTOCOLS (2016)

Article Multidisciplinary Sciences

Live single-cell laser tag

Loic Binan et al.

NATURE COMMUNICATIONS (2016)

Article Biochemistry & Molecular Biology

Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci

Erin B. Styles et al.

CELL SYSTEMS (2016)

Article Biochemistry & Molecular Biology

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

Yolanda T. Chong et al.

Article Biochemistry & Molecular Biology

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

Allon M. Klein et al.

Article Biochemistry & Molecular Biology

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Evan Z. Macosko et al.

Article Multidisciplinary Sciences

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

Silvana Konermann et al.

NATURE (2015)

Article Multidisciplinary Sciences

Spatially resolved, highly multiplexed RNA profiling in single cells

Kok Hao Chen et al.

SCIENCE (2015)

Article Chemistry, Multidisciplinary

Photostick: a method for selective isolation of target cells from culture

Miao-Ping Chien et al.

CHEMICAL SCIENCE (2015)

Article Biochemistry & Molecular Biology

Genome-scale quantitative characterization of bacterial protein localization dynamics throughout the cell cycle

Nathan J. Kuwada et al.

MOLECULAR MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

Luke A. Gilbert et al.

Article Biotechnology & Applied Microbiology

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library

Hiroko Koike-Yusa et al.

NATURE BIOTECHNOLOGY (2014)

Article Multidisciplinary Sciences

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

Ophir Shalem et al.

SCIENCE (2014)

Article Multidisciplinary Sciences

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

Tim Wang et al.

SCIENCE (2014)

Article Multidisciplinary Sciences

Highly Multiplexed Subcellular RNA Sequencing in Situ

Je Hyuk Lee et al.

SCIENCE (2014)

Article Multidisciplinary Sciences

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

Takashi Nagano et al.

NATURE (2013)

Article Biochemical Research Methods

In situ sequencing for RNA analysis in preserved tissue and cells

Rongqin Ke et al.

NATURE METHODS (2013)

Article Multidisciplinary Sciences

Composability of regulatory sequences controlling transcription and translation in Escherichia coli

Sriram Kosuri et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

RNA-Guided Human Genome Engineering via Cas9

Prashant Mali et al.

SCIENCE (2013)

Article Multidisciplinary Sciences

Multiplex Genome Engineering Using CRISPR/Cas Systems

Le Cong et al.

SCIENCE (2013)

Article Biotechnology & Applied Microbiology

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

Eilon Sharon et al.

NATURE BIOTECHNOLOGY (2012)

Article Multidisciplinary Sciences

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

Martin Jinek et al.

SCIENCE (2012)

Article Biochemistry & Molecular Biology

Robust Growth of Escherichia coli

Ping Wang et al.

CURRENT BIOLOGY (2010)

Article Multidisciplinary Sciences

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

Justin B. Kinney et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

The Genetic Landscape of a Cell

Michael Costanzo et al.

SCIENCE (2010)

Article Microbiology

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

Andrew L. Goodman et al.

CELL HOST & MICROBE (2009)

Article Biochemistry & Molecular Biology

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

Gemma C. Langridge et al.

GENOME RESEARCH (2009)

Article Biochemical Research Methods

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

Tim van Opijnen et al.

NATURE METHODS (2009)

Article Multidisciplinary Sciences

Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung

Jeffrey D. Gawronski et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Review Genetics & Heredity

The art and design of genetic screens: RNA interference

Michael Boutros et al.

NATURE REVIEWS GENETICS (2008)

Article Biochemistry & Molecular Biology

Monitoring dynamics of single-cell gene expression over multiple cell cycles

Scott Cookson et al.

MOLECULAR SYSTEMS BIOLOGY (2005)

Article Multidisciplinary Sciences

Global analysis of protein localization in budding yeast

WK Huh et al.

NATURE (2003)

Article Cell Biology

Subcellular localization of the yeast proteome

A Kumar et al.

GENES & DEVELOPMENT (2002)

Article Multidisciplinary Sciences

Systematic genetic analysis with ordered arrays of yeast deletion mutants

AHY Tong et al.

SCIENCE (2001)

Article Multidisciplinary Sciences

A synthetic oscillatory network of transcriptional regulators

MB Elowitz et al.

NATURE (2000)