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Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development

ABSTRACT: Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development

PROVIDER: PRJNA524331 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8633090_1.fastq.gz	Fastqsanger.gz
	SRR8633090_2.fastq.gz	Fastqsanger.gz
	SRR8633100.fastq.gz	Fastqsanger.gz
	SRR8633120.fastq.gz	Fastqsanger.gz
	SRR8633130.fastq.gz	Fastqsanger.gz

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Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development [set 2]

Project description:Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development [set 2]

| PRJNA524333 | ENA

Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development [set 1]

Project description:Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development [set 1]

| PRJNA524332 | ENA

Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development.

Project description:Studies in vertebrates have outlined conserved molecular control of definitive endoderm (END) development. However, recent work also shows that key molecular aspects of human END regulation differ even from rodents. Differentiation of human embryonic stem cells (ESCs) to END offers a tractable system to study the molecular basis of normal and defective human-specific END development. Here, we interrogated dynamics in chromatin accessibility during differentiation of ESCs to END, predicting DNA-binding proteins that may drive this cell fate transition. We then combined single-cell RNA-seq with parallel CRISPR perturbations to comprehensively define the loss-of-function phenotype of those factors in END development. Following a few candidates, we revealed distinct impairments in the differentiation trajectories for mediators of TGFβ signaling and expose a role for the FOXA2 transcription factor in priming human END competence for human foregut and hepatic END specification. Together, this single-cell functional genomics study provides high-resolution insight on human END development.

| S-EPMC6525305 | biostudies-literature

Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development [set 2]

Project description:Studies in vertebrates have outlined conserved molecular control of definitive endoderm (END) development. Yet, recent work also shows that key molecular aspects of human END regulation differ even from rodents. Differentiation of human pluripotent stem cells (hPSCs) to END offers a tractable system to study the molecular basis of normal and defective human-specific END development. Here, we interrogated dynamics in chromatin accessibility during differentiation of hPSCs to END, predicting DNA-binding proteins that may drive this cell fate transition. We then combined single-cell RNA-seq with parallel CRISPR-perturbations to comprehensively define the loss-of-function phenotype of those factors in END development. Following a few candidates, we revealed distinct impairments in the differentiation trajectories for mediators of TGFβ signaling and expose a role for the FOXA2 transcription factor in priming human END competence for human foregut and hepatic endoderm specification. Together, this single-cell functional genomics study provides high-resolution insight on human END development.

2019-04-16 | GSE127201 | GEO

Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development [set 1]

2019-04-16 | GSE127199 | GEO

Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-04-16 | GSE127202 | GEO

Genome-wide CRISPRi screening of Eubacterium limosum

Project description:Genome-wide CRISPRi screening of Eubacterium limosum

| PRJEB49804 | ENA

CRISPRi screening of Synechocystis

Project description:Pooled CRISPRi screening of the cyanobacterium Synechocystis sp. PCC 6803 for enhanced growth, tolerance, and chemical production

| PRJEB35238 | ENA

Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi

Project description:RNA-seq analysis to support CRISPRi functional genomics screening.

2019-02-22 | GSE126544 | GEO

Comparison of non-specific transcriptional effects of CRISPRi effector proteins by RNA-seq

Project description:CRISPR interference (CRISPRi) genetic screens use programmable repression of gene expression to systematically explore questions in cell biology and genetics. However, wider adoption of CRISPRi screening has been constrained by the large size of single guide RNA (sgRNA) libraries and lack of consensus on the choice of CRISPRi effector proteins. Here, we address these challenges to present next-generation CRISPRi sgRNA libraries and effectors. First, we combine empiric sgRNA selection with a dual sgRNA library design to generate an ultra-compact, highly active CRISPRi sgRNA library. Next, we rigorously compare CRISPRi effectors to show that the recently published Zim3-dCas9 provides an optimal balance between strong on-target knockdown and minimal nonspecific effects on cell growth or the transcriptome. Finally, we engineer a suite of cell lines which stably express Zim3-dCas9 and demonstrate robust on-target knockdown across these cell lines. Our results and publicly available reagents establish best practices for CRISPRi genetic screening.

2022-06-03 | GSE205147 | GEO

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