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Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [single-cell RNA-seq]

ABSTRACT: Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [single-cell RNA-seq]

PROVIDER: PRJNA789277 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17239852_1.fastq.gz	Fastqsanger.gz
	SRR17239852_2.fastq.gz	Fastqsanger.gz
	SRR17239853_1.fastq.gz	Fastqsanger.gz
	SRR17239853_2.fastq.gz	Fastqsanger.gz

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Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1

Project description:Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1

| PRJNA789272 | ENA

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [bulk RNA-seq]

Project description:Purpose: To identify differential expressed genes for loss of function of Mycn in zebrafish Methods: wild-type and mycn mutant zebrafish embryos were collected for RNA sequencing at 48 hpf (hours post fertilisation) and 72 hpf Results: We found 85 (overlapped) down-regulated genes in mycn mutant embryos at 48 hpf and 72 hpf (padj < 0.1, log2 fold change < 0) Conclusions: 85 down-regulated genes were identified

2021-12-17 | GSE191001 | GEO

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 (RNA-seq and Ribo-seq)

Project description:Purpose: To systematically investigate the molecular mechanisms resulting from Mycn loss-of-function. Methods: Approximately 30 mycn mutant or WT zebrafish embryos at 72 hpf (hours post fertilization) were harvested . Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000074) according to the manufacturer’s protocol for 10000 cells recovery. Results: More than 3,000 genes showed reduced tranlation efficiency in Mycn mutant. Conclusions: mTOR signaling was reduced in Mycn mutant.

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Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [single-cell RNA-seq]

Project description:Purpose: To systematically investigate the phenotypes resulting from Mycn loss-of-function at a higher resolution. Methods: Approximately 30 mycn mutant or WT zebrafish embryos at 72 hpf (hours post fertilization) were harvested . Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000074) according to the manufacturer’s protocol for 10000 cells recovery. Results: A total of 25,886 single-cell transcriptomes were collected after stringent quality control measures. Conclusions: 27 Cell types were identified by intergrating two datasets and 9 subclusters were obtained by reclustering intestinal cells.

2021-12-17 | GSE191002 | GEO

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [bulk RNA-seq]

Project description:Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [bulk RNA-seq]

| PRJNA789278 | ENA

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1

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

2021-12-17 | GSE191003 | GEO

LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy (Polysome sequencing)

Project description:High expression of LIN28B is associated with aggressive malignancy and poor survival. Here, probing MYCN-amplified neuroblastoma as a model system, we show that LIN28B expression is associated with enhanced cell migration in vitro and invasive and metastatic behavior in murine xenografts. Sequence analysis of the polyribosome fraction of LIN28B-expressing neuroblastoma cells revealed let-7 independent enrichment of transcripts encoding components of the translational and ribosomal apparatus, particularly those with higher adenine/uridine (AU)-content, and depletion of transcripts of neuronal developmental programs. We further show that LIN28B utilizes both its cold shock and zinc finger RNA binding domains to preferentially interact with MYCN-induced transcripts of the ribosomal complex, enhancing their translation. These data demonstrate that LIN28B couples the MYCN-driven transcriptional program to enhanced ribosomal translation, thereby implicating LIN28B as a post-transcriptional driver of the metastatic phenotype.

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LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy (RNA-Seq)

Project description:High expression of LIN28B is associated with aggressive malignancy and poor survival. Here, probing MYCN-amplified neuroblastoma as a model system, we show that LIN28B expression is associated with enhanced cell migration in vitro and invasive and metastatic behavior in murine xenografts. Sequence analysis of the polyribosome fraction of LIN28B-expressing neuroblastoma cells revealed let-7 independent enrichment of transcripts encoding components of the translational and ribosomal apparatus, particularly those with higher Adenine/Uridine (AU)-content, and depletion of GC-rich transcripts of neuronal developmental programs. We further show that LIN28B utilizes both its cold shock and zinc finger RNA binding domains to preferentially interact with MYCN-induced transcripts of the ribosomal complex, enhancing their translation. These data demonstrate that LIN28B couples the MYCN-driven transcriptional program to enhanced ribosomal translation, thereby implicating LIN28B as a post-transcriptional driver of the metastatic phenotype.

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LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy (RIP-Seq)

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