Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribosome profiling analysis of neuroblastoma cells in response to amidino-rocaglate treatment

ABSTRACT: Ribosome profiling analysis of neuroblastoma cells in response to amidino-rocaglate treatment

PROVIDER: PRJNA1088608 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28361540_1.fastq.gz	Fastqsanger.gz
	SRR28361540_2.fastq.gz	Fastqsanger.gz
	SRR28361541_1.fastq.gz	Fastqsanger.gz
	SRR28361541_2.fastq.gz	Fastqsanger.gz
	SRR28361542_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Ribosome profiling analysis of neuroblastoma cells in response to amidino-rocaglate treatment

Project description:MYCN-amplified neuroblastoma cells exhibit upregulation of translation regulation factors and ribosome biogenesis proteins as a result of MYCN-driven transcriptional amplification. Here, we treated MYCN-amplified and non-amplified neuroblastoma cells with a novel translation inhibitor, amidino-rocaglate CMLD12824, to compare the defects in translational efficiency.

2024-06-25 | GSE261760 | GEO

PAR-CLIP analysis of neuroblastoma cells in response to amidino-rocaglate treatment

Project description:MYCN-amplified neuroblastoma cells exhibit upregulation of translation initiation factors as a result of MYCN-driven transcriptional amplification, including the RNA helicase eIF4A1. Here, we treated MYCN-amplified patient derived xenograft (PDX) neuroblastoma cells with a novel translation initiation inhibitor, amidino-rocaglate CMLD12824, to analyze the impact on the global pattern of eIF4A1 binding to mRNA compared to the naive condition.

2024-06-25 | GSE261761 | GEO

PAR-CLIP analysis of neuroblastoma cells in response to amidino-rocaglate treatment

Project description:PAR-CLIP analysis of neuroblastoma cells in response to amidino-rocaglate treatment

| PRJNA1088607 | ENA

TPX2 as key downstream target of the eIF4A controlled translational program in MYCN driven neuroblastoma [MYCN_CutAndRun]

Project description:Current therapies for neuroblastoma are often ineffective and survivors suffer from severe long-term therapy related side-effects, underscoring the need for identification of novel drugging strategies. We performed an in-depth evaluation of phenotypic and molecular responses following exposure of neuroblastoma cells to the rocaglate CR-1-31-B, scrutinizing its mode-of-action through integrative ribosome footprinting and shotgun proteome profiling. We could show that CR-1-31-B significantly reduces tumor growth in vivo without apparent toxicity. By means of combined ribosome footprint and transcriptome analysis we could show that CR-1-31-B treatment induces downregulates factors involved in the G2/M checkpoint, while upregulated targets are enriched for oxidative phosphorylation pathway components and DNA repair. At the proteome level, CR-1-31-B revealed downregulation of a FOXM1 driven gene signature, with TPX2 as prominent marker. Knockdown of TPX2 leads to reduced neuroblastoma cell confluence and elevated levels of DNA damage. In conclusion, our data support CR-1-31-B as a potent novel therapeutic agent in neuroblastoma.

2026-02-01 | GSE246722 | GEO

TPX2 as key downstream target of the eIF4A controlled translational program in MYCN driven neuroblastoma[RNA-Seq]

2026-02-01 | GSE246725 | GEO

Ribosome profiling following AZD1775 treatment

Project description:Ribosome profiling following AZD1775 10 hour treatment in RPE1 TP53- cells

| PRJEB93983 | ENA

TPX2 as key downstream target of the eIF4A controlled translational program in MYCN driven neuroblastoma

Project description:Current therapies for neuroblastoma, a pediatric tumor arising from immature sympathoblast progenitors of the peripheral sympathetic nervous system, are often ineffective and most survivors suffer from severe long-term therapy related side-effects, underscoring the need for identification of novel drugging strategies with limited toxicity. We performed for the first time an in-depth phenotypic and molecular evaluation of pharmacological eIF4A inhibition in neuroblastoma using the rocaglate CR31B, scrutinizing its mode-of-action through a comprehensive and integrated shotgun proteome profiling and combined ribosome/RNA-seq footprinting approach. Short-term treatment of neuroblastoma cells with CR31B significantly affected viability within the very low nanomolar concentration range. Notably, ribosome footprinting following short-term CR31B exposure (6 hours) revealed amongst others strong enrichment for transcripts encoding proteins involved in N-glycan biosynthesis amongst the downregulated hits, while upregulated targets are enriched for oxidative phosphorylation pathway components. Shotgun proteome profiles during long-term (24h-48h-72h) CR31B exposure revealed a strong enrichment of a FOXM1 driven signature amongst the downregulated hits, a key regulator implicated in cell cycle control and DNA damage response in neuroblastoma. Last, we could show that CR31B significantly reduces tumor growth in vivo without apparent toxicity in a neuroblastoma PDX model. In conclusion, we present CR31B as a potent novel potent therapeutic agent in neuroblastoma.

2026-02-01 | GSE216192 | GEO

TPX2 as key downstream target of the eIF4A controlled translational program in MYCN driven neuroblastoma

2026-02-01 | GSE216191 | GEO

The effect of the Rocaglate on the macrophage gene expression

Project description:We report the analysis of the differential genes in mouse macrophages treated with the 100 nM of the Rocaglate vs untreated macrophages.

2018-10-11 | GSE113085 | GEO

Transcriptomic analysis of neuroblastoma cells in response to Earle's balanced salt solution treatment

Project description:Neuroblastoma, the most common extracranial solid malignancy in infants and young children, originates from aberrant neural crest cells and accounts for 10-15% of childhood cancer deaths. However, the underlying mechanisms regulating neuroblastoma progression remain to be determined. To investigate the mechanisms regulating tumorigenesis and aggressiveness, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma SH-SY5Y cells in response to treatment with Earle's balanced salt solution (EBSS) free of amino acids. The results showed that 1118 and 1392 genes were respectively elevated or reduced in SH-SY5Y cells after EBSS treatment. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to EBSS treatment in human neuroblastoma cells, and these findings will help us understand the pathogenesis of neuroblastoma progression.

2025-05-30 | GSE294551 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data