GEO DataSets

(Submitter supplied) Analyses of the effect of CRISPR/CAS9 mediated knock out of the EMT-transcription factor SNAI2 on the mRNA expression profile of human neuroblastoma SH-SY5Y cells to identify genes that are differentially expressed upon loss of SNAI2. Results provide insight into genes that are repressed by SNAI2 in neuroblastoma cells under normal culture conditions, where loss of SNAI2 enhances the expression of genes involved in biological processes such as neuron development and neuron differentiation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: TXT

(Submitter supplied) Analysis of the effect of shRNA-mediated knockdown of TRPM7 on gene expression levels in SH-SY5Y and SH-EP2 human neuroblastoma cells. Results were used for the identification of neural-crest-associated transcription factors that were affected by TRPM7 knockdown.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10904

8 Samples

Download data: TXT

(Submitter supplied) Purpose: To identify differntially expressed transcripts in TP-0903 treated embryos that impair cranila NC EMT and cell migration in zebrafish embryos Methods: zebrafish embryos treated at 13 hpf with 5-7uM TP-0903 and DMSO for 1-, 4- and 8-hrs at 28°C. 35 embryos were collected for each treatment. Results: TP-0903 increases expression of several retinoic acid target genes including genes from within the retinoid pathway Conclusions: TP-0903 causes a direct increase in RA signaling that impairs cranial NC EMT and cell migration in zebrafihs embryos

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14875 GPL18413

24 Samples

Download data: TXT

(Submitter supplied) Our data demonstrate that CARM1 is required for transcriptional activation of a subset of retinoic acid (RA) target genes in J1 murine embryonic stem cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: XLSX

(Submitter supplied) The main scientific objective of the project was to investigate whether Lamin A/C could be involved in neuroblastoma differentiation. Moreover, taking into account the significance of differentiation stage in the neuroblastoma tumor progression we have also studied a possible role of Lamin A/C in the tumorigenesis of this neuronal cancer. As differentiating stimulus we used the all-trans retinoic acid (RA), the most effective compound which has been shown to induce differentiation in neuroblastoma cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

6 Samples

Download data: TXT

(Submitter supplied) We report the ChIP-Seq results of SNAI2 in several different conditions which include: SNAI2 binding in both control and SNAI2 knockdown cells to demonstrate specificity of the binding. SNAI2 ChIP-Seq was also performed in SNAI2 or control LACZ overexpressing cells cultured in growth medium as well as LACZ or SNAI2 overexpressing cells in differentiation medium.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: TXT

(Submitter supplied) 1. Keratinocytes infected with retroviruses expressing control or SNAI2 shRNAs were cultured in growth medium and Affymetrix HG-U133 plus 2.0 arrays were used to determine global gene expression profiles. 2. Keratinocytes infected with retroviruses overexpressing LACZ or SNAI2 were cultured in growth medium and Affymetrix HG-U133 plus 2.0 arrays were used to determine global gene expression profiles.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL, CHP

(Submitter supplied) Neuroblastoma (NB) arises from neural crest cells (NCCs) secondary to a block in differentiation. Retinoic acid (RA) differentiation therapy has limited therapeutic efficacy, and the mechanisms preventing terminal differentiation remain elusive. We found that the chromatin modifier CHAF1A restricts neuronal differentiation and promotes NB oncogenesis. CHAF1A blocks NC differentiation into mature neurons in both human NCCs and zebrafish models. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

12 Samples

Download data: CEL

(Submitter supplied) This series represents murine dorsal neural tube bisected along the midline with one half from each embryo used for control and the other half treated with 10-6M RA dissolved in ethanol for 6, 12, 24 or 48 h. For 6 h exposures, the explants were cultured overnight on fibronectin coated 35mm dishes (Biocoat, Becton Dickinson Labware, Bedford, MA) in DMEM with 10% horse serum in order to allow for sufficient outgrowth of neural crest cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS773

Platform:

GPL81

27 Samples

Download data: CEL, EXP

Expression profiling of cranial neural crest exposed to 1 uM retinoic acid (RA) at various lengths of time up to 48 hours. Neural crest obtained from 8.5 days postcoitum ICR embryos. Results provide insight into developmental pathways affected upon exposure to teratogenic concentrations of RA.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 agent, 4 time sets

Platform:

GPL81

Series:

GSE1588

27 Samples

Download data: CEL, EXP

(Submitter supplied) The aim of the dataset was to study on genome-wide level the effect of Notch inhibition in gene expression on neural crest differentiation of human embryonic stem cells under chemically defined conditions.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data

(Submitter supplied) Bone marrow (BM) mesenchymal stem and progenitor cells (MSPCs) are a critical constituent of the hematopoietic stem cell (HSC) niche. Previous studies have suggested that the zinc-finger epithelial-mesenchymal transition transcription factor Snai2 (also known as Slug) regulated HSCs autonomously. Here, we show that Snai2 expression in the BM is restricted to the BM stromal compartment where it regulates the HSC niche. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) A neuroblasoma cell line, NB-1, was treated with a DNA demethylating agents (5-aza-2'-deoxycytidine: 5-aza-dC). Genome-wide DNA methylation was analyzed using the Infinium HumanMethylation450 BeadChip.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

2 Samples

Download data: IDAT

(Submitter supplied) A neuroblasoma cell line, TGW, was treated with a DNA demethylating agents (5-aza-2'-deoxycytidine: 5-aza-dC). Genome-wide DNA methylation was analyzed using the Infinium Human MethylationEPIC BeadChip.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

2 Samples

Download data: IDAT

(Submitter supplied) A neuroblastoma cell line, NB-1, was treated with mock, a DNA demethylating agent (5-aza-2'-deoxycytidine: 5-aza-dC), a synthetic retinoic acid (tamibarotene: TBT), and the combination of 5-aza-dC and TBT. A genome-wide gene expression analysis was performed using SurePrint G3 Human Gene Expression 8 x 60K v2 Microarray.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17077

4 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

36 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Neuroblastoma cell lines (Kelly, BE2C) were subject to chromatin profiling by ATAC-seq ATAC-seq analysis of Neuroblastoma cell lines +/- shAhR knockdown

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) AhR promotes dedifferentiation in MYCN amplified neuroblastoma

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: CSV

(Submitter supplied) The goals of this study are to compare transcriptome profiling (mRNA level) and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups, and the stem markers of nueral crest progenitors were upregulated in mutants.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

8 Samples

Download data: TXT

(Submitter supplied) Embryonic malignant transformation is concomitant to organogenesis, often affecting multipotent and migratory progenitors. Neuroblastoma (NB) is an emblematic example, arising from neural crest progenitors and characterized by a high heterogeneity and a widely disseminated clinical presentation. Metastatic triggers from the embryonic environment are suspected but yet unknown due to limited investigation access in patients and current models. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT