Expression data of human neuroblastoma tissue samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE16237 | GEO | 2009/09/01
SECONDARY ACCESSION(S): PRJNA115119
REPOSITORIES: GEO
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Project description:The prognosis of the patients with neuroblastoma largely depends on the biological characteristics. Neuroblastoma tissues obtained before any treatments were analyzed for gene expression using Affymetrix array. We used microarrays to detail the global programme of gene expression distinguishing tumor biology of neuroblastoma tissues from the prognosis of the patients. Experiment Overall Design: 51 neuroblastoma samples were selected those resected from the patients who died of tumor progression and those whose tumor regressed or matured spontaneously. Total RNA was extracted from these tissues samples and hybridized on Affymetrix microarrays. We sought to obtain genes to distinguish unfavorable tumors from favorable tumors.
2009-09-15 | E-GEOD-16237 | biostudies-arrayexpress
Project description: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.
2014-06-24 | GSE46583 | GEO
Project description: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. We selected several murine neuroblastoma tumors for RNA extraction and hybridization on Affymetrix microarrays. We generated three groups of tumors: 10 MYCN amplified tumors, 11 MYCN amplified/ALK F1174L tumors and 10 MYCN amplified/ALK R1275Q tumors.
2014-06-24 | E-GEOD-46583 | biostudies-arrayexpress
Project description:We used an inducible ShRNA system and microarrays to detail the global programme of gene expression underlying neuroblastoma differentiation upon CHAF1A silencing . CHAF1A is a subunit of the Chromatin Assembly Factor-1 (CAF1) and regulates H3K9-trimethylation. High expression of CHAF1A strongly correlates with neuroblastoma poor prognosis and loss-of-function drives neuronal differentiation in vitro and in vivo.
2013-11-01 | GSE51978 | GEO
Project description:We used an inducible ShRNA system and microarrays to detail the global programme of gene expression underlying neuroblastoma differentiation upon CHAF1A silencing . CHAF1A is a subunit of the Chromatin Assembly Factor-1 (CAF1) and regulates H3K9-trimethylation. High expression of CHAF1A strongly correlates with neuroblastoma poor prognosis and loss-of-function drives neuronal differentiation in vitro and in vivo. Total RNA was isolated using RNAeasy kit from IMR32 cells transduced with inducible CHAF1A ShRNA. Gene expression profiling was performed in neuroblastoma cells upon CHAF1A silencing over time course (0, 5, and 10 days) in triplicate.
2013-11-01 | E-GEOD-51978 | biostudies-arrayexpress
Project description: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 an F1178L Alk mutation corresponding to the ALK F1174L mutation observed in neuroblastoma patients We used microarrays to detail the global programme of gene expression underlying the impact of ALK F1178L mutation on sympathetic nervous system ganglia
2014-06-24 | GSE46584 | GEO
Project description: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 an F1178L Alk mutation corresponding to the ALK F1174L mutation observed in neuroblastoma patients We used microarrays to detail the global programme of gene expression underlying the impact of ALK F1178L mutation on sympathetic nervous system ganglia We selected sympathetic nervous system ganglia (superior cervical and stellate ganglia) for RNA extraction and hybridization on Affymetrix microarrays. We profiled a total number of 12 Po (4 Wt; 4 Hz; 4 Ho) and 5 P18 (3 Wt; 2 Hz)
2014-06-24 | E-GEOD-46584 | biostudies-arrayexpress
Project description:Reference1: Ohira M, Oba S, Nakamura Y, Isogai E, Kaneko S, Nakagawa A, Hirata T, Kubo H, Goto T, Yamada S, Yoshida Y, Fuchioka M, Ishii S, Nakagawara A. Expression profiling of human primary Expression profiling using a tumor-specific cDNA microarray predicts the prognosis of intermediate risk neuroblastomas. Cancer Cell. 2005 Apr;7(4):337-50. To predict the prognosis of neuroblastoma patients and choose a better therapeutic protocol, we developed a cDNA microarray carrying 5340 genes obtained from primary neuroblastomas and examined 136 tumor samples. We made a probabilistic output statistical classifier that provided a high accuracy in prognosis prediction (89% at 5 years) and a highly reliable method to validate it. Kaplan-Meier analysis indicated that the patients in an intermediate group defined by existing markers are divided by microarray into two further groups with 5 year survivals for 36% and 89% of patients (p < 10(-4)), i.e., with unfavorably and favorably predicted neuroblastomas, respectively. According to these results, we developed a gene subset chip for a clinical tool, for which our classifier exhibited 88% prediction accuracy. Datasets: neuroblastomas by CCC-NB200-Chip: GSM42338-GSM42387 Expression profiling of human primary neuroblastomas by CCC-NB5000-Chip: GSM42391-GSM42526 Keywords = Neuroblastoma
2005-05-12 | E-GEOD-2283 | biostudies-arrayexpress
Project description: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. We performed a genome-wide analysis of a large number of neuroblastoma samples, consisting of varying disease stages, permitted us to obtain a comprehensive registry of genomic lesions in neuroblastoma.
2008-10-10 | GSE12494 | GEO
Project description:Reference1: Ohira M, Oba S, Nakamura Y, Isogai E, Kaneko S, Nakagawa A, Hirata T, Kubo H, Goto T, Yamada S, Yoshida Y, Fuchioka M, Ishii S, Nakagawara A. Expression profiling of human primary Expression profiling using a tumor-specific cDNA microarray predicts the prognosis of intermediate risk neuroblastomas. Cancer Cell. 2005 Apr;7(4):337-50. To predict the prognosis of neuroblastoma patients and choose a better therapeutic protocol, we developed a cDNA microarray carrying 5340 genes obtained from primary neuroblastomas and examined 136 tumor samples. We made a probabilistic output statistical classifier that provided a high accuracy in prognosis prediction (89% at 5 years) and a highly reliable method to validate it. Kaplan-Meier analysis indicated that the patients in an intermediate group defined by existing markers are divided by microarray into two further groups with 5 year survivals for 36% and 89% of patients (p < 10(-4)), i.e., with unfavorably and favorably predicted neuroblastomas, respectively. According to these results, we developed a gene subset chip for a clinical tool, for which our classifier exhibited 88% prediction accuracy. Datasets: neuroblastomas by CCC-NB200-Chip: GSM42338-GSM42387 Expression profiling of human primary neuroblastomas by CCC-NB5000-Chip: GSM42391-GSM42526 Keywords = Neuroblastoma Keywords: other
2005-05-12 | GSE2283 | GEO