Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-Content Imaging-Based Pooled CRISPR Screens in Mammalian Cells

ABSTRACT: High-Content Imaging-Based Pooled CRISPR Screens in Mammalian Cells

PROVIDER: PRJNA658532 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12492000.fastq.gz	Fastqsanger.gz
	SRR12492001.fastq.gz	Fastqsanger.gz
	SRR12492002.fastq.gz	Fastqsanger.gz
	SRR12492003.fastq.gz	Fastqsanger.gz
	SRR12492004.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 26

Similar Datasets

High-Content Imaging-Based Pooled CRISPR Screens in Mammalian Cells

Project description:We developed a microscopy-based approach, which we name optical enrichment, to select cells displaying a particular CRISPR-induced phenotype by automated imaging-based computation, mark them by photo-activation of an expressed photo-activatable fluorescent protein, and then isolate the fluorescent cells using fluorescence-activated cell sorting (FACS). One proof-of-principle screen, a nuclear size screen, a FSC screen and a H2B-mGFP screen were performed to validate the method.

2021-01-12 | GSE156623 | GEO

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

Project description:Pooled CRISPR screens with imaging on microRaft arrays reveals stress granule-regulatory factors

| PRJNA587094 | ENA

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

Project description:CRISPR (clustered regularly interspaced short palindromic repeats)-based gene inactivation provides a powerful means for linking genes to particular cellular phenotypes. CRISPR-based screening typically uses large genomic pools of single guide RNAs (sgRNAs). However, this approach is limited to phenotypes that can be enriched by chemical selection or FACS sorting. Here, we developed a microscopy-based approach, which we name optical enrichment, to select cells displaying a particular CRISPR-induced phenotype by automated imaging-based computation, mark them by photoactivation of an expressed photoactivatable fluorescent protein, and then isolate the fluorescent cells using fluorescence-activated cell sorting (FACS). A plugin was developed for the open source software μManager to automate the phenotypic identification and photoactivation of cells, allowing ∼1.5 million individual cells to be screened in 8 h. We used this approach to screen 6,092 sgRNAs targeting 544 genes for their effects on nuclear size regulation and identified 14 bona fide hits. These results present a scalable approach to facilitate imaging-based pooled CRISPR screens.

| S-EPMC7821101 | biostudies-literature

Pooled CRISPR screens in human intestinal organoids [CRISPR screens]

Project description:Pooled CRISPR screens in human intestinal organoids [CRISPR screens]

| PRJNA608420 | ENA

Pooled CRISPR screens in human macrophages

Project description:Pooled CRISPR screens in human macrophages

| PRJNA893203 | ENA

Pooled CRISPR screens in human intestinal organoids

Project description:Pooled CRISPR screens in human intestinal organoids

| PRJNA608374 | ENA

Scalable, compressed phenotypic screening using pooled perturbations (PDAC screens)

Project description:High-throughput phenotypic screens leveraging biochemical perturbations and high-content readouts are poised to advance therapeutic discovery, yet they remain constrained by limitations of scale. To address this, we establish a method of pooling exogenous perturbations followed by computational deconvolution to compress a screen’s required sample, labor, and financial input. We benchmark the approach with a bioactive small molecule library and a high-content imaging readout, demonstrating the feasibility and increased efficiency of compressed experimental designs compared to conventional approaches. To prove generalizability, we apply compressed screening in two different biological discovery campaigns. In the first, we use early-passage pancreatic cancer organoids to map transcriptional responses to alibrary oftumor-microenvironmentrecombinant protein ligands. We uncover reproducible phenotypic shifts induced by specific ligands that are distinct from canonical reference signatures and uniquely correlate with clinical outcome.In the second, we examine the modulatory effects of a known mechanism of action chemical compound library on primary human peripheral blood mononuclear cell immune responses. Through contrastive analyses, we identify molecules that potentiate and/or inhibit cell-type specific transcriptional features, uncover pleiotropic effects for individual compounds across diverse cell types, and realize a systems-level view of drug responses. In sum, our approach empowers phenotypic screens with information-rich readouts to advance drug discovery efforts as well as basic biological inquiry.

2024-05-13 | GSE267243 | GEO

Pooled CRISPR screens in human intestinal organoids [ATAC-seq]

Project description:Pooled CRISPR screens in human intestinal organoids [ATAC-seq]

| PRJNA608811 | ENA

Pooled CRISPR screens in human intestinal organoids [RNA-seq]

Project description:Pooled CRISPR screens in human intestinal organoids [RNA-seq]

| PRJNA608809 | ENA

Pooled CRISPR screens in human intestinal organoids [CUT&RUN]

Project description:Pooled CRISPR screens in human intestinal organoids [CUT&RUN]

| PRJNA608810 | ENA