GEO DataSets

(Submitter supplied) Intra-tumour heterogeneity is increasingly appreciated as a determinant of tumour recurrence. Several tumour types were recently found to include phenotypically divergent cell types, reflecting lineage development stages (1,2,3). Lineage identity has been proposed to ensue super-enhancer (SE)-associated transcription factor (TF) networks (4,5), but their role in intra-tumour heterogeneity is unknown. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20148 GPL16791

31 Samples

Download data: BED

(Submitter supplied) Transition between differentiation states in development occurs swift but the mechanisms leading to epigenetic and transcriptional reprogramming are poorly understood. The pediatric cancer neuroblastoma includes adrenergic (ADRN) and mesenchymal (MES) tumor cell types, which differ in phenotype, super-enhancers (SEs) and core regulatory circuitries. These cell types can spontaneously interconvert, but the mechanism remains largely unknown. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL570

26 Samples

Download data: BED, CEL

(Submitter supplied) Expression analysis of xenograft tumors of ADRN cell line SH-SY5Y with doxycycline-inducible NOTCH3-IC was used to study transcriptional reprogramming to a MES state in vivo.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) Expression analysis of ADRN cell line SH-SY5Y with transient- or permanent doxycycline-inducible NOTCH3-IC expression was used to study reversibility of transcriptional reprogramming.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

5 Samples

Download data: CEL

(Submitter supplied) Expression analysis of ADRN cell line SH-SY5Y with doxycycline-inducible NOTCH3-IC was used to study transcriptional reprogramming to a MES state.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

9 Samples

Download data: CEL

(Submitter supplied) Cell line pairs with different phenotypes were isolated from individual patients to study intra-tumor heterogeneity in neuroblastoma

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

13 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20148 GPL570 GPL16791

69 Samples

Download data: BED, CEL

(Submitter supplied) PRRX1 is expressed in mesenchymal-type neuroblastoma cells. Over-expression of PRRX1 in adrenergic-type cell line was used to study reprogramming towards a mesenchymal lineage.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

17 Samples

Download data: CEL

(Submitter supplied) Cell line pairs with different phenotypes were isolated from individual patients to study intra-tumor heterogeneity in neuroblastoma

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data

(Submitter supplied) Purpose: Infection of neuroblastoma cell liner BE(2)N with a retroviral vector that overexpressed Dn-hTERT caused the conversion of these cells from adrenergic morphology to one that resembles mesenchymal cells. During prolonged passage, down-regulation of Dn-hTERT expression caused a reversal in cell morphology (i.e., from mesenchymal to adrenergic cells). The goal of this study is to characterize the transcriptomes of BE(2)N during the morphologic conversion and reversal and determine if the transcription changes are consistent with previously defined ADRN and MES signature genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: TXT

(Submitter supplied) Purpose: Treatment of neuroblastoma cell liner BE(2)N is known to convert these cells from adrenergic morphology to one that resembles mesenchymal cells. The goal of this study is to characterize the transcriptomes of BE(2)N during the conversion process and determine if the transcription changes are consistent with previously defined ADRN and MES signature genes. Methods: BE2N cells were treated with DMSO for 26 days or with 10µM BrdU for 5, 11, 20 and 26 days. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

5 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL28038 GPL20301 GPL23227

44 Samples

Download data: BED, BEDPE, BW, NARROWPEAK

(Submitter supplied) RNA-seq analysis was performed in a Neuroblastoma cell line (GI-MEN) to analyze gene expression changes after ASCL1 ot other TFs overexpression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

8 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis was performed in a Neuroblastoma cell line (GI-MEN) to analyze gene expression changes after ASCL1 overexpression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

4 Samples

Download data: TXT

(Submitter supplied) Cut & Run analysis was performed in an neuroblastoma cell line to analyze DNA bindings of ASCL1-tag-HA in GI-MEN ASCL1-tag-HA cells and GI-MEN ASCL1-tag-HA+4TFs cells; analyze DNA bindings of MYCN, PHOX2B and H3K27ac in, GI-MEN 4TFs cells, and GI-MEN ASCL1-tag-HA+4TFs cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: BED, BW

(Submitter supplied) H3K27ac HiChIP analysis was performed in GI-MEN DOX-ASCL1 cells to analyze active chromatin-chromatin interactions in GI-MEN DOX-ASCL1 cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL28038

2 Samples

Download data: BED, BEDPE

(Submitter supplied) ChIP-seq analysis was performed in an neuroblastoma cell line to analyze DNA bindings of H3K27ac in GI-MEN DOX-ASCL1 cells and ASCL1-HA in GI-MEN DOX-ASCL1-tag-HA cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: BED, BW

(Submitter supplied) ATAC-seq analysis was performed in an neuroblastoma cell line to analyze chromatin opening of Gi-MEN cells under four different conditions.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: BW, NARROWPEAK