ChIP-seq-based analysis of i) K27me3 promoter coverage and ii) enhancer elements in neuroblastoma cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE80197 | GEO | 2016/09/08
SECONDARY ACCESSION(S): PRJNA318261
REPOSITORIES: GEO
Similar Datasets
Project description:The impact of drugs inhibiting DNA methylation (5-aza-2'-deoxycytodine, DAC) and EZH2 (EPZ-6438) on H3K27me3 coverage was analyzed in two neuroblastoma cell lines. Parallel analyses investigated associated changes in RNA expression and DNA methylation. The neuroblastoma cell lines Be(2)-C and IMR5-75 were treated with a combination of DAC and EPZ-6438. Controls were treated with solvent (DMSO). H3K27me3 ChIP seq was done to investigate treatment-related changes of this mark. In addition, H3K4me3 and H3K27ac ChIP seq was done in DMSO treated samples to identify putative regulatory regions.
2016-09-08 | E-GEOD-80445 | biostudies-arrayexpress
Project description:The impact of drugs inhibiting DNA methylation (5-aza-2'-deoxycytodine, DAC) and EZH2 (EPZ-6438) on H3K27me3 coverage was analyzed in two neuroblastoma cell lines. Parallel analyses investigated associated changes in RNA expression and DNA methylation.
2016-09-08 | GSE80445 | 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
2005-05-12 | E-GEOD-2283 | 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 Keywords: other
2005-05-12 | GSE2283 | GEO
Project description:RNA expression profiles of 105 primary neuroblastomas derived from customized 4 x 44k oligonucleotide microarrays (Agilent Technologies). These profiles are part of an integrative study combining genomewide epigenetic profiles with transcriptome data of the same neuroblastoma cohort. Tumors were derived from 40 low-risk, 9 intermediate-risk and 56 high-risk patients. Transcription profiles of 105 primary neuroblastomas derived from customized 4 x 44k oligonucleotide microarrays (Agilent Technologies)
2016-09-08 | E-GEOD-73517 | biostudies-arrayexpress
Project description:Migratory embryonal neuroblasts give rise to several tissues, including the sympathetic nervous system (SNS). Neuroblastomas are paediatric tumours of the peripheral SNS with a highly variable prognosis. We observed that high NOTCH3 expression in neuroblastomas correlated with a poor prognosis. Expression of a NOTCH3 transgene in neuroblastoma cells induced many motility genes and conferred a highly motile phenotype. Expression of these motility genes strongly correlated with NOTCH3 expression in neuroblastomas and many other tumours, suggesting a general role for NOTCH3 in regulation of these genes. Silencing of NOTCH3 or genes of the Notch-processing M-NM-3-secretase complex induced apoptosis in all neuroblastoma cell lines tested. These data suggest that NOTCH3 is a key-regulator of motility, and indispensable for survival of neuroblastoma cells. Time-course experiments of NOTCH3IC induction in two independent clones (c6 and c8), with 9 or 8 time points, respectively.
2013-08-06 | E-GEOD-16477 | biostudies-arrayexpress
Project description:Migratory embryonal neuroblasts give rise to several tissues, including the sympathetic nervous system (SNS). Neuroblastomas are paediatric tumours of the peripheral SNS with a highly variable prognosis. We observed that high NOTCH3 expression in neuroblastomas correlated with a poor prognosis. Expression of a NOTCH3 transgene in neuroblastoma cells induced many motility genes and conferred a highly motile phenotype. Expression of these motility genes strongly correlated with NOTCH3 expression in neuroblastomas and many other tumours, suggesting a general role for NOTCH3 in regulation of these genes. Silencing of NOTCH3 or genes of the Notch-processing γ-secretase complex induced apoptosis in all neuroblastoma cell lines tested. These data suggest that NOTCH3 is a key-regulator of motility, and indispensable for survival of neuroblastoma cells.
2013-08-06 | GSE16477 | GEO
Project description:Integrated analysis of array-based comparative genome hybridization (aCGH) and gene expression profiling was conducted by using primary neuroblastomas. This submission corresponds the latter gene expression data. Keywords: other Thirty mass screening-detected and 40 sporadic neuroblastomas were analyzed by both aCGH and gene expression profiling. A UCSF BAC array carrying 2,464 clones was used for the former experiment. For the latter experiment, an in-house cDNA microarray, carrying 5,340 cDNAs obtained from the oligo-capping cDNA libraries generated from anonymous neuroblastoma tissues, were used. Preparation of RNA, hybridization, reading of spots, and statistical analyses were conducted as reported previously [Ohira M, et al. Cancer Cell 2005;7:337-50.]. This series corresponds expression profiles for 40 sporadic neuroblastomas.
2007-09-05 | E-GEOD-5779 | biostudies-arrayexpress
Project description:Neuroblastomas are characterized by recurrent segmental and/or numerical chromosomal abberations such as MYCN-amplification or 11q-deletion. To further elucidate recurrent chromosomal alterations, 16 neuroblastoma cell lines were investigated.
2022-11-10 | GSE209728 | GEO
Project description:dCas9-guided recruitment of the proximity ligation enzyme BirA* to the promoter region of RRM2 in SKNBE2c neuroblastoma cells.
2022-08-12 | PXD029630 | Pride