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Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [CHIP-seq]

ABSTRACT: Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [CHIP-seq]

PROVIDER: PRJNA955099 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24152517_1.fastq.gz	Fastqsanger.gz
	SRR24152517_2.fastq.gz	Fastqsanger.gz
	SRR24152518_1.fastq.gz	Fastqsanger.gz
	SRR24152518_2.fastq.gz	Fastqsanger.gz
	SRR24152519_1.fastq.gz	Fastqsanger.gz

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Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [screen]

Project description:Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [screen]

| PRJNA955098 | ENA

Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [screen]

Project description:Enteroendocrine cells (EECs) are hormone-producing cells residing in the epithelium of stomach, small intestine (SI) and colon. EECs regulate various aspects of metabolic activity including insulin levels, satiety, gastrointestinal secretion and motility. The generation of different EEC lineages of the SI is incompletely understood. We now report a TFome-wide CRISPR knockout screen in adult human intestinal organoids to identify dominant transcription factors controlling EEC differentiation. ZNF800 is discovered as a master repressor for endocrine lineage commitment, which particularly restricts enterochromaffin cell differentiation by directly controlling an endocrine TF network centered on PAX4. Thus, organoid models allow unbiased functional SCRISPR screens for genes that program cell differentiation.

2023-10-27 | GSE229584 | GEO

Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation.

Project description:Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation.

| PRJNA955079 | ENA

Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [CHIP-seq]

2023-10-27 | GSE229583 | GEO

Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [scRNA-seq]

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Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [scRNA-seq]

Project description:Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [scRNA-seq]

| PRJNA955102 | ENA

Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation.

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

2023-10-26 | GSE229586 | GEO

Identification of functional enteroendocrine regulators by real-time single-cell differentiation mapping

Project description:Homeostatic regulation of the intestinal enteroendocrine lineage hierarchy is a poorly understood process. We resolved transcriptional changes during enteroendocrine differentiation in real-time at single-cell level using a novel knock-in allele of Neurog3, the master regulator gene briefly expressed at the onset of enteroendocrine specification. A bi-fluorescent reporter, Neurog3Chrono, measures time from the onset of enteroendocrine differentiation and enables precise positioning of single-cell transcriptomes along an absolute time axis. This approach yielded a definitive description of the enteroendocrine hierarchy and its sub-lineages, uncovered differential kinetics between sub-lineages, and revealed time-dependent hormonal plasticity in enterochromaffin and L-cells. The time-resolved map of transcriptional changes predicted multiple novel molecular regulators. Nine of these were validated by conditional knockout in mice or CRISPR-modification in intestinal organoids. Six novel candidate regulators (Sox4, Rfx6, Tox3, Myt1, Runx1t1 and Zcchc12) yielded specific enteroendocrine phenotypes. Our time-resolved single cell transcriptional map presents a rich resource to unravel enteroendocrine differentiation.

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Project description:We generated knock-in mice expressing GFP under the control of the endogenous GIP (Glucose-dependent Insulinotropic Polypeptide) promoter that enable the isolation of a purified population of small intestine K cells. Using RNA-Seq, we comprehensively characterized the transcriptomes of GIP-GFP cells as well as the entire enteroendocrine lineage derived from Neurogenin3 (Ngn3)-expressing progenitors. We interrogated the whole transcriptome of FACS-isolated small intestine GIPGFP cells using high-throughput mRNA sequencing. We also obtained the global gene expression patterns of the entire enteroendocrine cell lineage as well as the non-enteroendocrine cell population, comprising enterocytes, goblet cells and Paneth cells. To achieve this, small intestine epithelial cells from male mice resulting from the breeding of Neurogenin3 (Ngn3)-Cre mice with ROSA26-LoxP-STOP-LoxP-tomato indicator mice were isolated based on Tomato fluorescence and negative staining for CD45. Due to the small cell numbers, we constructed each of the three RNA-Seq libraries (GIPGFP, Ngn3TOMATO, and Ngn3-) using a pool of equal amounts of individual RNA samples without RNA amplification.

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Single cell and bulk RNA sequencing of Enteroendocrine cells from human hormone reporter organoids

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