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Links from GEO DataSets

Items: 20

1.

MicroRNA expression profiling of Ewing sarcoma cell lines

(Submitter supplied) Ewing’s sarcoma family tumors (ESFT) are the second most common bone malignancy in children and young adults, characterized by the expression of a unique chromosomal translocation, that in 85% of cases lead to the expression of the EWS-FLI-1 fusion protein. ESW-FLI-1 functions as an aberrant transcription factor that can both induce and suppress its target genes. We have recently demonstrated that microRNA (miRNA) 145 is a direct EWS-FLI-1 target implicated in ESFT development. more...
Organism:
Homo sapiens; Mus musculus; Rattus norvegicus; synthetic construct
Type:
Non-coding RNA profiling by array
Platform:
GPL10993
4 Samples
Download data: TXT
Series
Accession:
GSE29085
ID:
200029085
2.

Gene expression analysis of human pediatric mesenchymal stem cells (hpMSCs) upon expression of EWS-FLI-1

(Submitter supplied) Cancer stem cells (CSCs) display plasticity and self-renewal properties reminiscent of normal tissue stem cells, but the events responsible for their emergence remain obscure. We recently identified CSCs in Ewing sarcoma family tumors (ESFTs) and showed that they retain mesenchymal stem cell (MSC) plasticity. In the present study, we addressed the mechanisms that underlie ESFT CSC development. We show that the EWS-FLI-1 fusion gene, associated with 85%-90% of ESFTs and believed to initiate their pathogenesis, induces expression of the embryonic stem cell (ESC) genes OCT4, SOX2, and NANOG in human pediatric MSCs (hpMSCs) but not in their adult counterparts. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
8 Samples
Download data: CEL
Series
Accession:
GSE31215
ID:
200031215
3.

A zebrafish transgenic model of Ewing's Sarcoma reveals conserved mediators of EWS-FLI1 tumorigenesis

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL1319
12 Samples
Download data: CEL
Series
Accession:
GSE31217
ID:
200031217
4.

The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes Ewing's-type tumors in zebrafish

(Submitter supplied) The fusion oncoprotein EWS-FLI1 arises from a t(11;22)(q24;q12) chromosomal translocation and causes Ewing's Sarcoma, a malignant bone tumor. The mechanism whereby EWS-FLI1 transforms cells is unknown. Somatic, mosaic expression of human EWS-FLI1 in zebrafish from the heat shock promoter [Tg(HSP:EWS-FLI1)] caused small round blue cell tumors (SRBCTs) similar to human Ewing's sarcoma. We performed microarray studies comparing zebrafish SRBCTs to another tumor type, zebrafish malignant peripheral nerve sheath tumors (MPNSTs). more...
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL1319
6 Samples
Download data: CEL
Series
Accession:
GSE31186
ID:
200031186
5.

The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes developmental defects in zebrafish embryos

(Submitter supplied) The fusion oncoprotein EWS-FLI1 arises from a t(11;22)(q24;q12) chromosomal translocation and causes Ewing's Sarcoma, a malignant bone tumor. The mechanism whereby EWS-FLI1 transforms cells is unknown. We made germline transgenic zebrafish expressing human EWS-FLI1 under the control of the heat shock promoter. Induction of EWS-FLI1 expression causes multiple defects in embryonic development. We compared gene expression in control and transgenic EWS-FLI1 zebrafish. more...
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL1319
6 Samples
Download data: CEL
Series
Accession:
GSE31185
ID:
200031185
6.

A molecular function map of Ewing’s Sarcoma

(Submitter supplied) EWS-FLI1 is a chimeric ETS transcription factor that is, due to a chromosomal rearrangement, specifically expressed in Ewing’s sarcoma family tumors (ESFT) and is thought to be the initiating event in the development of the disease. Previous genomic profiling experiments have identified a number of EWS-FLI1 regulated genes and genes that discriminate ESFT from other sarcomas, but so far a comprehensive analysis of EWS-FLI1 dependent molecular functions characterizing this aggressive cancer is lacking. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL96
10 Samples
Download data: CEL
Series
Accession:
GSE14543
ID:
200014543
7.

RNA immunoprecipitation (RIP)-Chip analysis for EWS-bound mRNA

(Submitter supplied) Although EWS/FLI-1 fusion protein is responsible for most Ewing’s sarcoma family tumors (ESFT), the function of native EWS remains largely unknown. Here, we first showed that EWS repressed protein expression in a tethering assay. mRNAs bound to EWS were determined by RNA-immunoprecipitation Chip assay, and one of them, proline-rich Akt substrate of 40 kDa (PRAS40) mRNA, directly interacted with EWS. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
8 Samples
Download data: CEL
Series
Accession:
GSE29313
ID:
200029313
8.

Hypoxia modulates EWS-FLI1 transcriptional signature and enhances malignant properties of Ewing’s tumor cells in vitro

(Submitter supplied) Hypoxia is an important condition in the tumor cell microenvironment and approximately 1-1.5% of the genome is transcriptionally responsive to hypoxia with hypoxia-inducible factor-1 (HIF-1) as a major mediator of transcriptional activation. Tumor hypoxia is associated with a more aggressive phenotype of many cancers in adults, but data on pediatric tumors are scarce. By immunohistochemical analysis, HIF-1α expression was readily detectable in 18/28 primary Ewing´s sarcoma family tumors (ESFT), a group of highly malignant bone-associated tumors in children and young adults, which encouraged us to study the effect of hypoxia on ESFT cell lines in vitro. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platforms:
GPL570 GPL571
12 Samples
Download data: CEL
Series
Accession:
GSE19197
ID:
200019197
9.

A673 Ewing's sarcoma cells: stable-knockdown and inducible-rescue time course experiments

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL96
23 Samples
Download data
Series
Accession:
GSE4565
ID:
200004565
10.

A673 inducible-rescue experiment

(Submitter supplied) A673 Ewing's sarcoma cells, with inducible EWS/FLI cDNA, harboring the EF-2-RNAi retrovirus, induced (or uninduced) for the indicated time period. Keywords: time course
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL96
15 Samples
Download data
Series
Accession:
GSE4563
ID:
200004563
11.

A673 Stable-Knockdown

(Submitter supplied) A673 Ewing's sarcoma cells containing either control RNAi retroviral constructs (luc-RNAi), or RNAi retroviral constructs targeting the endogenous EWS/FLI fusion transcript (either EF-2-RNAi or EF-4-RNAi). Keywords: Expression analysis of RNAi knockdown of endogenous EWS/FLI
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL96
8 Samples
Download data
Series
Accession:
GSE4560
ID:
200004560
12.

Ewing Sarcoma cell lines treated with mithramycin

(Submitter supplied) The study aims to define gene expression changes associated with mithramycin treatment of Ewing Sarcoma cell lines.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
12 Samples
Download data: CEL
Series
Accession:
GSE25127
ID:
200025127
13.

RUNX3 Facilitates Growth of Ewing Sarcoma Cells

(Submitter supplied) Ewing sarcoma is an aggressive pediatric small round cell tumor that predominantly occurs in bone. Approximately 85% of Ewing sarcomas harbor the EWS/FLI fusion protein, which arises from a chromosomal translocation, t(11:22)(q24:q12). EWS/FLI interacts with numerous lineage-essential transcription factors to maintain mesenchymal progenitors in an undifferentiated state. We previously showed that EWS/FLI binds the osteogenic transcription factor RUNX2 and prevents osteoblast differentiation. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
2 Samples
Download data: TXT
14.

Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription

(Submitter supplied) Using EWS-FLI and its parental transcription factor, FLI1, we created a unique experimental system to address questions regarding the genomic mechanisms by which chimeric transcription factors cause cancer. We found that in tumor cells, EWS-FLI targets regions of the genome distinct from FLI1, despite identical DNA-binding domains. In primary endothelial cells, however, EWS-FLI and FLI1 demonstrate similar targeting. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL5188 GPL10999
32 Samples
Download data: BED, CEL
15.

Expression data from A673 cell line treated with compounds at several doses and time points

(Submitter supplied) An increasing number of cancer-associated mutations have been identified. Unfortunately, little therapy today exploits these tumor-specific genetic lesions. Often, the resulting oncoproteins have been intractable to easy manipulation with current small molecule screening approaches. To overcome this impasse, we developed an expression-based approach to small molecule library screening. We applied this platform to the discovery of modulators of the activity of EWS/FLI, the Ewing sarcoma associated oncoprotein. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS2733
Platform:
GPL4685
68 Samples
Download data: CEL
Series
Accession:
GSE6930
ID:
200006930
16.
Full record GDS2733

Cytosine arabinoside effect on Ewing's sarcoma cell line: time course and dose response

Analysis of Ewing’s sarcoma A673 cells for up to 5 days after treatment with cytosine arabinoside (ARA-C) at EC50 or twice the EC50. ARA-C identified as a modulator of the Ewing’s sarcoma EWS/FLI fusion protein. Results provide insight into the specificity of the response of A673 cells to ARA-C.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 4 agent, 3 dose, 3 time sets
Platform:
GPL4685
Series:
GSE6930
68 Samples
Download data: CEL
17.

EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma

(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; Other; Third-party reanalysis
Platforms:
GPL20301 GPL22790
60 Samples
Download data
Series
Accession:
GSE185132
ID:
200185132
18.

EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (4C)

(Submitter supplied) Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL22790
10 Samples
Download data: RDS
Series
Accession:
GSE185131
ID:
200185131
19.

EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (RNA-Seq)

(Submitter supplied) Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Third-party reanalysis
Platform:
GPL20301
4 Samples
Download data: BW, TXT, XLSX
20.

EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (Cut&Tag III)

(Submitter supplied) Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis
Download data: BED, BW, NARROWPEAK, TXT
Series
Accession:
GSE185128
ID:
200185128
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