GEO DataSets

(Submitter supplied) We performed gene expression profiling by Affymetrix primeview array in both NGP CRISPR control cells and NGP ALK(LF655del) cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16043

6 Samples

Download data: CEL

(Submitter supplied) Neuroblastoma is an embryonal neoplasm that remains of dramatic prognosis in its aggressive forms. Activating mutations of the ALK tyrosine kinase receptor have been identified in sporadic and familial cases of this cancer. We generated knock-in mice carrying the two most frequent Alk mutations observed in neuroblastoma patients. We used microarrays to detail the global programme of gene expression underlying the impact of ALK mutations on neuroblastoma formation in a MYCN amplified background.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16225

31 Samples

Download data: CEL

(Submitter supplied) The RET gene has been identified previously as a target of activated ALK at the mRNA level in both human neuroblastoma cell lines and primary tumors as well as in murine tumors driven by mutated Alk and MYCN. Moreover, it has been shown that tumor growth of murine TH-MYCN/KI Alkmut tumors was impaired upon Ret inhibition by the vandetanib inhibitor, suggesting RET as a therapeutic target in ALK mutated neuroblastoma. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL16368

6 Samples

Download data: CEL, TXT

(Submitter supplied) The expression profiles of 64 neuroblastic tumors (mainly neuroblastoma) were determined on Affymetrix chips HG U133 Plus 2.0.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

64 Samples

Download data: CEL

(Submitter supplied) High anaplastic lymphoma kinase (ALK) protein levels may be correlated with an unfavorable prognosis in neuroblastoma (NBL) patients, regardless of ALK mutation status. We therefore examined the correlation between levels of ALK, phosphorylated ALK (pALK) and downstream signaling proteins and response to ALK inhibition in a large panel of both ALK mutated (MUT) and wild type (WT) NBL cell lines. Six of the nineteen NBL cell lines had a point mutation and four an amplification of the ALK gene. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

17 Samples

Download data: CEL, CHP

(Submitter supplied) The prognosis of advanced stage neuroblastoma patients remains poor and, despite intensive therapy, the 5-year survival rate remains less than 50%. We previously identified histone deacetylase (HDAC) 8 as an indicator of poor clinical outcome and a selective drug target for differentiation therapy in vitro and in vivo. Here we performed kinome-wide RNAi screening to identify genes that are synthetically lethal with HDAC8 inhibitors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

6 Samples

Download data: IDAT

(Submitter supplied) Neuroblastoma (NB) is comprised of a mixture of neuroblastic N-type cancer cells, and Schwannian stromal S-type cells. Sublines of N- and S-type cells were isolated from an early passage of SK-N-SH NB cell line. RNA-Seq analysis was conducted on slected N- and S-type cells in order to define their unique expression profiles.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

4 Samples

Download data: TXT

(Submitter supplied) Neuroblastoma in advanced stages is among the most intractable pediatric cancers, even with the recent therapeutic advances. Neruroblastoma harbours a variety of genetic changes, including a high frequency of MYCN amplification, loss of heterozygosity in 1p36 and 11q, and gain of genetic material from 17q, all of which have been implicated in the pathogenesis of neuroblastoma. However, the scarcity of reliable molecular targets has hampered the development of effective therapeutic agents targeting neuroblastoma. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL2005 GPL2004 GPL3718

262 Samples

Download data: CEL, CHP

(Submitter supplied) Chromosome 1p LOH was seen in one-third of cases. LOH events on chromosomes 11q and 1p were generally accompanied by copy number loss. The one exception was on chromosome 11p, where LOH in all 4 cases was accompanied by normal copy number or diploidy, implying uniparental disomy. Amplification of MYCN was also noted, and also, amplification of a second gene, ALK, in a single case. Keywords: SNP array analysis

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL1266 GPL2641

44 Samples

Download data: CEL, TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of Y95 phosphorylation on SMAD4-mediated transcription in response to TGF-b signals. The goals of this study are to compare transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: mRNA profiles of HaCaT parental and SMAD4 KO cells stably expressing wild-type SMAD4 (WT), Y95E or Y95F mutant, and GFP (as control) under with or without TGF-b were generated by deep sequencing, using Illumina HiSeq X Ten. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

10 Samples

Download data: BEDGRAPH