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RNA-seq analysis after LMO1 or MYCN knockdown in Kelly cells

ABSTRACT: RNA-seq analysis after LMO1 or MYCN knockdown in Kelly cells

PROVIDER: PRJNA486907 | ENA |

REPOSITORIES: ENA

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RNA-seq analysis after LMO1 or MYCN knockdown in Kelly cells

Project description:RNA-seq analysis was performed in Kelly neuroblastoma cell line to analyze gene expression changes after LMO1 or MYCN knockdown.

2019-11-10 | GSE118823 | GEO

LMO1 Synergizes with MYCN to Promotes Neuroblastoma Initiation and Metastasis

Project description:High levels of LMO1 expression synergizes with MYCN to accelerate neuroblastomagenesis, enhance disease penetrance and promote widespread metastasis in zebrafish. Transcriptomic analysis of human neuroblasotma cells with programed expression of LMO1 vs vector control or neuroblastoma cells with differential endogenous LMO1 expression revealed that gene signitures affecting tumor cell-extracellular matrix interaction are significantly associated with high levels of LMO1 expression. Our findings provide compelling evidence for a major pathogenic role of LMO1 in MYCN-driven neuroblastoma.

2017-07-31 | GSE90087 | GEO

RNA-seq analysis after knockdown of ASCL1 gene in Kelly cells

Project description:RNA-seq analysis was performed in Kelly neuroblastoma cell line to analyze gene expression changes after ASCL1 knockdown.

2019-11-10 | GSE132698 | GEO

ASCL1 is directly activated by the LMO1 and MYCN oncogenes and is a master regulator of the differentiation program in neuroblastoma

Project description:Neuroblastoma is an embryonal tumor of the peripheral sympathetic nervous system. Elevated expression of the transcription factor LMO1 and the polymorphisms within this gene are associated with the susceptibility to develop neuroblastoma. LMO1 has been implicated as an oncogene in T-cell acute lymphoblastic leukemia; however, the transcriptional targets regulated by this protein in neuroblastoma cells are unknown. Here, we identify the genes and molecular pathways controlled by LMO1 in neuroblastoma cells. ChIP-seq analysis revealed that LMO1-bound regions are frequently co-occupied by GATA3 and MYCN proteins and are associated with active histone marks in neuroblastoma cells. RNA-seq analysis demonstrated that LMO1 regulates gene expression in a tumor type-specific manner. One high-confidence target gene directly regulated by LMO1 and MYCN is ASCL1, which is more highly expressed in adrenergic subtype of neuroblastoma cells as compared to normal neuronal cells. High levels of ASCL1 expression are associated with inferior overall survival in primary human neuroblastoma cases. ChIP-seq analysis identified a regulatory element controlling ASCL1 expression that is bound by LMO1, MYCN and the members of the core regulatory circuitry in neuroblastoma cells. Furthermore, ASCL1 is required for neuroblastoma cell growth and regulates genes responsible for repression of neuronal cell differentiation. Taken together, our results implicate ASCL1 as a critical downstream target of LMO1 in the molecular pathogenesis of neuroblastoma.

2019-11-09 | GSE120074 | GEO

Gene Expression Analysis of the Neuroblastoma Kelly Cell Line

Project description:Gene expression profililing of the MYCN-amplified Kelly cell line

2011-06-18 | E-MEXP-3121 | biostudies-arrayexpress

Gene expression profile of human neuroblastoma cell line SHSY-5Y after LMO1 knockdown

Project description:To dissect molecular pathways regulated by LMO1 in neuroblastoma, we performed microarray gene expression profiling in a neuroblastoma cells (SHSY-5Y) after LMO1 knockdown.

2019-11-10 | GSE130747 | GEO

Genome wide chromatin changes in TAE684 sensitive and resistant Kelly cells.

Project description:We performed ChIP-seq on MYCN in both TAE684 sensitive and resistant Kelly cells.

2019-08-07 | GSE115249 | GEO

Genome-wide binding of MYCN protein in MYCN-amplified neuroblastoma cell lines

Project description:The MYCN locus is amplified in about half of high-risk neuroblastoma tumors. To identify genomic loci occupied by MYCN protein in the MYCN-amplified neuroblastoma cell lines NGP, Kelly and NB-1643, we performed chromatin immunoprecipitation coupled with Next-Generation Sequencing (ChIP-seq) using an anti-MYCN antibody.

2017-08-02 | GSE94782 | GEO

Global transcriptome analysis in the MYCN-amplified neuroblastoma cell line IMR5-75 upon inducible MYCN-knockdown

Project description:Inducible MYCN-knockdown, followed by RNA-seq analysis in the MYCN-amplified neuroblastoma cell line IMR5-75, reveals profound time-dependent transcriptome changes. For modulation of MYCN levels, stable neuroblastoma cell models were used where MYCN can be downregulated via vector-based hairpin RNA induction upon addition of 1Âµg/ml tetracycline (IMR5-75-shMYCN. From cells treated either with tetracycline or solvent (ethanol), RNA was isolated at time points 6 hours, 12 hours and 24 hours. Experiments were done in duplicates. RNA was sequenced.

2016-09-08 | E-GEOD-80397 | biostudies-arrayexpress

RNA-seq of IMR-5/75 neuroblastoma cell line upon TBX2 and/or MYCN knockdown

Project description:RNA-seq upon TBX2, MYCN or combination of TBX2 and MYCN knockdown in the neuroblastoma cell line IMR-5/75. Cells were transduced with two different shRNAs (shTBX2_2 and shTBX2_4) targeting TBX2 and a non-targeting control (NTC), and selected with puromycin. Cells were treated with doxycycline for shMYCN induction (with DOX or not). Analysis was performed three days upon TBX2 knockdown and two days upon MYCN knockdown, including six biological replicates per condition.

2018-08-16 | E-MTAB-6568 | biostudies-arrayexpress

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