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

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

PROVIDER: PRJNA524332 | 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
	SRR8633091_1.fastq.gz	Fastqsanger.gz
	SRR8633091_2.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

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

| PRJNA524331 | ENA

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: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

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

2019-04-16 | GSE127202 | GEO

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

RNA-seq of CSMD1 enhancer CRISPRi in LUHMES cells and differentiated neurons

Project description:we performed lentiviral CRISPR interference (CRISPRi) by recruiting dCas9 fused with the KRAB domain to the CSMD1 enhancer (fam3) in the neuronal precursor cell line – Lund human mesencephalic (LUHMES). Given that the expression of CSMD1 was not detectable in LUHMES cells we differentiated these cells into neurons. Differentiated neurons with CRISPRi of CSMD1 enhancer showed significantly higher expression of CSMD1 than control.

2022-06-30 | E-MTAB-8027 | biostudies-arrayexpress

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Project description:Genome-wide CRISPRi screening of Eubacterium limosum

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iPSC RNA-seq upon CRISPRn or CRISPRi manipulation

Project description:Assess the on- and off-target effects of dox-inducible CRISPR/Cas9 and CRISPRi constructs in a human iPS cell line. Transcript quantification of 3 cell lines, each plus or minus doxycycline and with or without specific single guide RNAs (sgRNAs), with 2 biological replicates each.

2016-01-19 | E-GEOD-76980 | biostudies-arrayexpress

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