GEO DataSets

(Submitter supplied) IL13Rα2 overexpression promotes metastasis of basal-like breast cancers IL13Rα2 depletion in highly metastatic breast cancer cells suppresses lung metastases formation by upregulating TP63 and decreasing their migratory potential

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

8 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Background: The basic helix-loop-helix transcription factor TWIST1 (Twist) is involved in embryonic cell lineage determination and mesodermal differentiation. There is evidence to indicate that Twist expression plays a role in breast tumor formation and metastasis, but the role of Twist in dysregulating pathways that drive the metastatic cascade is unclear. Importantly, the genes and pathways dysregulated by Twist in cell lines and mouse models have not been validated against data obtained from patient samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

11 Samples

Download data: CEL

(Submitter supplied) Subpopulations of MDA-MB-231 that exhibit different metastatic tropisms when injected into immuno-deficient mice. Also, a cohort of primary breast cancers surgically resected at the Memorial Sloan-Kettering Cancer Center (MSKCC). Keywords = Breast cancer Keywords = lung metastasis Keywords: parallel sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

121 Samples

Download data: CEL, EXP

(Submitter supplied) Long non-coding RNAs (lncRNA) have emerged as important regulators of gene expression at both the transcriptional and post-transcriptional levels. While altered expressions of lncRNAs have been observed in breast cancer (BCa) development, their roles in BCa progression and metastasis are still poorly understood. To identify novel BCa-associated lncRNA candidates, we have employed a high-density SNP array based approach to uncover lncRNA genes at intergenic region that are aberrantly expressed in BCa. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

6 Samples

Download data: CEL

(Submitter supplied) The survival of women with brain metastases (BM) from breast cancer remains very poor, and more than 80% will die within a year of their diagnosis. Here we define the function of IL13Rα2 in outgrowth of breast cancer brain metastases (BCBM) in vitro and in vivo, and postulate IL13Rα2 as a suitable therapeutic target for BM. Experimental design: We performed IHC staining of IL13Rα2 in BCBM to define its prognostic value. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28337

6 Samples

Download data: TXT

(Submitter supplied) Knockdown of BHLHE40 expression significantly reduced primary tumor growth and spontaneous lung metastasis in an orthotopic xenograft model of human breast cancer. Gene expression analysis implicated a role of BHLHE40 in hypoxia-induced exosomic secretion of Heparin Binding Epidermal Growth Factor HBEGF, which promotes cell survival and invasion. BHLHE40 induces HBEGF transcription by blocking DNA binding of HDAC1 and HDAC2.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) We examined whether SATB1 functions as a global gene regulator in order to maintain the aggressive phenotype of the MDA-MB-231 cell line. We compared the gene expression profiles between control_shRNA-MDA-MB-231 cells, which express SATB1 at high levels, and SATB1_shRNA1-MDA-MB-231 in which the level of SATB1 was greatly downregulated by RNAi technology. This comparative studies were performed using two different platforms (Codelink and Affymetrix genechip) with two culture conditions either on plastic dish (2D) or on matrigel (3D) which allows cells to form a breast-like morphology only for non-aggressive cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL3921 GPL4044

12 Samples

Download data: CEL, TXT

(Submitter supplied) Affymetrix expression profiling was used to evaluate the association between IL13Rα2 expression, and mesenchymal, proneural, classical and neural signature genes expression for glioma subclasses defined by Verhaak et al (Cancer Cell; 2010).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

26 Samples

Download data: CEL

(Submitter supplied) Breast cancer metastasis is the leading cause of breast cancer-related mortalities in women. Differential gene expression programs enriched in the primary tumor is able to distinguish patients that experience relapse to different organs. Epigenomic changes often underlie transcriptomic differences and give rise to stable phenotypes. However, the epigenomic differences present in organotropic metastasis remains underexplored. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: BW, TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL11154

30 Samples

Download data

(Submitter supplied) Breast cancer metastasis is the leading cause of breast cancer-related mortalities in women. Differential gene expression programs enriched in the primary tumor is able to distinguish patients that experience relapse to different organs. Epigenomic changes often underlie transcriptomic differences and give rise to stable phenotypes. However, the epigenomic differences present in organotropic metastasis remains underexplored. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: BED, BW, TXT

(Submitter supplied) Breast cancer metastasis is the leading cause of breast cancer-related mortalities in women. Differential gene expression programs enriched in the primary tumor is able to distinguish patients that experience relapse to different organs. Epigenomic changes often underlie transcriptomic differences and give rise to stable phenotypes. However, the epigenomic differences present in organotropic metastasis remains underexplored. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

15 Samples

Download data: BED, BW, TXT

(Submitter supplied) Abstract BACKGROUND: The basal-like breast cancer (BLBC) subtype is characterized by positive staining for basal mammary epithelial cytokeratin markers, lack of hormone receptor and HER2 expression, and poor prognosis with currently no approved molecularly-targeted therapies. The oncogenic signaling pathways driving basal-like tumorigenesis are not fully elucidated. METHODS: One hundred sixteen unselected breast tumors were subjected to integrated analysis of phosphoinositide 3-kinase (PI3K) pathway related molecular aberrations by immunohistochemistry, mutation analysis, and gene expression profiling. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

95 Samples

Download data: TXT

(Submitter supplied) By survival analysis of breast cancer patients, JMJD6 was found to be significantly associated with poor prognosis. Over-expression and knock-down of JMJD6 in breast cancer cell lines suggested a role in proliferation. In order to study the transcriptional events that occur following JMJD6 expression changes, siRNA-mediated knock-down of JMJD6 was performed in MCF-7 and MDA-MB231 and stable over-expression of JMJD6 was performed in MCF-7.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

28 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

142 Samples

Download data: BED

(Submitter supplied) We report high-throughput profiling of TRIM25 binding sites in triple negative breast cancer cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: BEDGRAPH

(Submitter supplied) We report high-throughput profiling of TRIM25 bound mRNA in triple negative breast cancer cells.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

6 Samples

Download data: BED

(Submitter supplied) Purpose: To identify regulatory proteins that are potential drivers of a coordinated breast cancer metastasis gene expression signatures. Methods: Knockdown of target genes in breast cancer cell lines was achieved using scramble and/or gene-specific siRNA (ON-TARGET SMARTpool, Thermo Scientific) and Lipofectamine RNAiMAX. 48h post transfection, total RNA was isolated from cell lines using the RNeasy Plus mini prep kit (Qiagen). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

128 Samples

Download data: TXT

(Submitter supplied) We sought to characterize methylome remodeling during regional metastasis. We profiled the DNA methylome (n=44) and transcriptome (n=36) of matched primary breast tumors and regional metastases.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

72 Samples

Download data: CEL

(Submitter supplied) We performed differential expression analyses from RNA-seq data derived from isogenic p53 wild-type and p53-knockdown triple negative breast tumors

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

7 Samples

Download data: TXT