GEO DataSets

(Submitter supplied) MYCN is a master regulator controlling many processes necessary for tumor cell survival. Here, we unravel a microRNA network that causes tumor suppressive effects in MYCN-amplified neuroblastoma cells. In profiling studies, histone deacetylase (HDAC) inhibitor treatment most strongly induced miR-183. Enforced miR-183 expression triggered apoptosis, and inhibited anchorage-independent colony formation in vitro and xenograft growth in mice. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8179

6 Samples

Download data: TXT

(Submitter supplied) Neuroblastoma is an embryonic solid tumor of neural crest origin and accounts for 11% of all cancer-related deaths in children. Novel therapeutic strategies are therefore urgently required. MYCN oncogene amplification, which occurs in 20% of neuroblastomas, is a hallmark of high risk. Here we aimed to exploit molecular mechanisms that can be pharmacologically addressed with epigenetically modifying drugs, such as histone deacetylase (HDAC) inhibitors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5263

Platform:

GPL10558

12 Samples

Download data: TXT

Analysis of BE(2)-C cells up to 72 hrs after transient transfection with construct pTRex-GRHL1. The three mammalian GRHL genes (GRHL1, -2, and -3) represent a highly conserved family of β-scaffold transcription factors. Results provide insight into the role of GRHL1 in neuroblastoma biology.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 protocol, 3 time sets

Platform:

GPL10558

Series:

GSE47407

12 Samples

Download data

(Submitter supplied) We studied transcriptional changes by Illumina HumanHT-12 v4 microarrays in 2 Neuroblastoma cell lines after i-BET-726 treatment

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS5364 GDS5365

Platform:

GPL10558

18 Samples

Download data: TXT

Analysis of SK-N-SH neuroblastoma (NB) cells treated with 0.1 or 1 uM I-BET726, a BET inhibitor. MYCN is unamplified in SK-N-SH. BET inhibitors display anti-proliferative activity in MYC driven hematologic cancer models. Results provide insight into the anti-proliferative activity of I-BET726 in NB.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 agent, 3 dose sets

Platform:

GPL10558

Series:

GSE47386

9 Samples

Download data

Analysis of CHP-212 neuroblastoma (NB) cells treated with 0.1 or 1 uM I-BET726, a BET inhibitor. MYCN is amplified in CHP-212. BET inhibitors display anti-proliferative activity in MYC driven hematologic cancer models. Results provide insight into the anti-proliferative activity of I-BET726 in NB.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 agent, 3 dose sets

Platform:

GPL10558

Series:

GSE47386

9 Samples

Download data

(Submitter supplied) The bromodomain inhibitor JQ1 and the histone deacetylase inhibitor panobinostat induce synergistic anticancer effects We analyzed whether JQ1 and panobinostat synergistically modulate gene expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

12 Samples

Download data: CEL

(Submitter supplied) Neuroblastomas are tumors of the developing peripheral sympathetic nervous system, which originates from the neural crest. Twenty percent of neuroblastomas show amplification of the MYCN oncogene, which correlates with poor prognosis. The MYCN transcription factor can activate and repress gene expression. To broaden our insight in the spectrum of genes down-regulated by MYCN, we generated gene expression profiles of the neuroblastoma cell lines SHEP-21N and SKNAS-NmycER, in which MYCN activity can be regulated. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

16 Samples

Download data: CEL, CHP

(Submitter supplied) Bromodomain inhibition comprises a promising therapeutic strategy in cancer, particularly for hematologic malignancies. To date, however, genomic biomarkers to direct clinical translation have been lacking. We conducted a cell-based screen of genetically-defined cancer cell lines using a prototypical inhibitor of BET bromodomains. Integration of genetic features with chemosensitivity data revealed a robust correlation between MYCN amplification and sensitivity to bromodomain inhibition. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

12 Samples

Download data: CEL

(Submitter supplied) Global miRNAs expression profilling of SK-N-BE(2)-C cells after dsRNA-mediated knockdown of MYCN

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) To identify the MYCN transcription factor binding sites across the genome, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using anti-MYCN and anti-IgG antibodies on a MYCN-amplified NB cell line, SK-N-BE(2)-C.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BED, TXT

(Submitter supplied) mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

88 Samples

Download data: CEL

(Submitter supplied) Gene expression data from BE(2)-C cells treated in triplicate with either vehicle (DMSO), 5 μM all-trans retinoic acid (ATRA), 1 mM valproic acid (VPA), or 5 μM ATRA + 1 mM VPA for 6, 24, or 72 hours. Genome-wide expression profiling was performed using Affymetrix U133A microarrays. While cytotoxic chemotherapy remains the hallmark of cancer treatment, intensive regimens fall short in many malignancies, including high-risk neuroblastoma. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4685

35 Samples

Download data: CEL

(Submitter supplied) Histone Deacetylase (HDAC) is known as a key regulator of cell development and cancer through deacetylation of histones as well as other proteins. Recent studies have shown that HDAC class 1 expression is sometimes highly elevated in the diagnosis of patients who appear to have strongly proliferating cancer. Among them, experiments were conducted to confirm the significance of the difference in the presence or absence of HDAC2.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

8 Samples

Download data: CEL, CHP

(Submitter supplied) Neuroblastoma is a common childhood cancer with almost a third of those affected still dying, thus new therapeutic strategies need to be explored. Current experimental therapies focus mostly on inhibiting oncogenic transcription factor signalling. Dysregulation of miRNAs has oncogenic or suppressive tumor functions in a variety of cancer, also including neuroblastoma. Therefore, we investigated the miRNA landscape in 97 neuroblastoma samples from different INSS stages, including MYCN-amplified (MNA) tumor samples.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15456

97 Samples

Download data: CSV

(Submitter supplied) Neuroblastoma, the most common extracranial pediatric solid tumor, is responsible for 15% of all childhood cancer deaths. Patients frequently present at diagnosis with metastatic disease, particularly to the bone marrow. Advances in therapy and understanding of the metastatic process have been limited due in part, to the lack of animal models harboring bone marrow disease. The widely employed transgenic model, the TH-MYCN mouse, exhibits limited metastasis to this site. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4617

Platform:

GPL1261

29 Samples

Download data: CEL

(Submitter supplied) Neuroblastoma, the most common extracranial pediatric solid tumor, is responsible for 15% of all childhood cancer deaths. Patients frequently present at diagnosis with metastatic disease, particularly to the bone marrow. Advances in therapy and understanding of the metastatic process have been limited due in part, to the lack of animal models harboring bone marrow disease. The widely employed transgenic model, the TH-MYCN mouse, exhibits limited metastasis to this site. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL16275

13 Samples

Download data: TXT

Analysis of primary abdominal neuroblastoma (NB) tumors from a metastatic NB model. This model recapitulates two alterations frequent observed in metastatic NB: MYCN overexpression and loss of caspase-8 expression. Results provide insight into the molecular mechanisms underlying metastatic NB.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 genotype/variation, 2 tissue sets

Platform:

GPL1261

Series:

GSE42548

29 Samples

Download data: CEL

(Submitter supplied) Nuclear deformability is an essential feature of migratory cells. Intercellular movement and migration in the extracellular space requires cells to squeeze through constrictions up to an order of magnitude smaller than the average diameter of their biggest and stiffest organelle. One field of study in which aberrant nuclear shapes and deformability are of particular interest is cancer, with abnormal nuclear structures described as a hallmark of the disease and an indicator of pathological progression, while increased nuclear deformability correlates with increased metastatic potential. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT