GEO DataSets

(Submitter supplied) We profiled primary breast cancer, nodal and liver metastatic tumours from three patients. At the time of initial diagnosis, all three patients presented with luminal breast cancer with adjacent nodal metastasis. They all received 5 years of enodrine therapy and all subsequently developed liver metastasis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) Acquired resistance to aromatase inhibitor (AI) therapy is a major clinical problem in the treatment of breast cancer. The detailed mechanisms of how tumour cells develop this resistance remain unclear. Here estrogen receptor ChIPseq analysis identifies adaptations of the ER in response to prolonged letrozole treatment.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9115 GPL11154 GPL10999

8 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) To assess the global effects of HOXC11 in endocrine resistant breast cancer cells we performed RNA-seq on LY2 cells which were transfected with either siRNA targeting HOXC11 (siHOXC11) or a scrambled negative control siRNA (scrHOXC11) in the presence of 4-OH-tamoxifen (10-8M). Knockdown was verified by Taq-man qRT-PCR prior to library preparation. RNA (10µg) was extracted using an Oligotex mRNA kit (Qiagen) as per manufacturer’s instructions (n=4). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

8 Samples

Download data: XLSX

(Submitter supplied) The seed-and-soil hypothesis was described over a century ago to describe why cancer cells (seeds) grow in certain organs (soil). Since then, the genetic properties that define the cancer cells have been heavily investigated, however, the genetic mediators within the organ microenvironment that mediate successful metastatic growth are less understood. In these studies, a set of human breast cancer patient-derived xenograft (PDX) metastasis models were utilized. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL22245

128 Samples

Download data: 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: WIG

(Submitter supplied) The steroid co-activator protein SRC-1 plays an important role in endocrine therapy resistant breast cancer. Its expression is associated with large high grade tumours, HER2 positivity, disease recurrence and resistance to endocrine therapy. While SRC-1 typically functions to activate gene expression, some evidence has pointed towards a potential role in repression. This study looks into the effects of a stable knockdown of SRC-1 in a tamoxifen resistant cell line, LY2, and the effects of this knock down on the methylation landscape.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: WIG

(Submitter supplied) The steroid co-activator protein SRC-1 plays an important role in endocrine therapy resistant breast cancer. Its expression is associated with large high grade tumours, HER2 positivity, disease recurrence and resistance to endocrine therapy. SRC-1's role in affecting the transcriptome of the breast cancer endocrine resistant setting is uncovered through this RNA-seq analysis of LY2 cells grown with or without the presence of SRC-1

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) We sought to identify genetic variants associated with disease relapse and failure to hormonal treatment in hormone-receptor positive breast cancer (HRPBC). We analyzed a series of HRPBC with distant relapse, by sequencing pairs (n=11) of tumors (primary and metastases) at >800X. Comparative genomic hybridization was performed as well. Top hits, based on the frequency of alteration and severity of the changes, were tested in the TCGA series. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL21613

16 Samples

Download data: TXT

(Submitter supplied) Breast cancer cells display preferences for specific metastatic sites including the bone, lung and liver. Metastasis is a complex process that relies, in part, on interactions between disseminated cancer cells and resident/infiltrating stromal cells that constitute the metastatic microenvironment. Distinct immune infiltrates can either impair the metastatic process or conversely, assist in the seeding, colonization and growth of disseminated cancer cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5666

Platform:

GPL7202

15 Samples

Download data: TXT

Analysis of parental mammary tumor cell line 4T1-derived metastatic populations isolated from liver, lung or bone. Results provide insight into molecular mechanisms associated with the different metastatic breast cancer sub-populations.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 5 cell type sets

Platform:

GPL7202

Series:

GSE62598

15 Samples

Download data: TXT

(Submitter supplied) Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across 850000 CpGsites in nine different breast cancer PDX models. Docetaxel resistant and residual disease PDX models were also analyzed

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL21145

70 Samples

Download data: CSV, IDAT, TXT

(Submitter supplied) SurePrint G3 Human Gene Expression Microarray v2 was used to obtain gene expression profiles of two different TNBC PDX models sensitive to docetaxel and in the docetaxel resistant TNBC PDX models derived from both initially sensitive.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16699

11 Samples

Download data: TXT

(Submitter supplied) Background: Despite advances in therapeutics, outcomes for hepatocellular carcinoma (HCC) remain poor and there is an urgent need for efficacious systemic therapy. Unfortunately, drugs that are successful in preclinical studies often fail in the clinical setting, and we hypothesize that this is due to functional differences between primary tumors and commonly used preclinical models. In this study, we attempt to answer this question by comparing tumor morphology and gene expression profiles between primary tumors, xenografts and HCC cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

30 Samples

Download data: CEL

(Submitter supplied) We investigated the global microRNA expression patterns in normal pancreas, pancreatic endocrine tumours and acinar carcinomas to evaluate their involvement in transformation and malignant progression of these tumour types.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL20949

44 Samples

Download data: GPR

(Submitter supplied) We investigated the global gene expression in a large panel of pancreatic endocrine tumours (PETs) aimed at identifying new potential targets for therapy and biomarkers to predict patient outcome.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20945

97 Samples

Download data: SPOT

(Submitter supplied) Introduction: Metastasis of breast cancer is the main cause of death in patients. Previous genome-wide studies have identified gene expression patterns correlated with cancer patient outcome, however these were mostly derived from whole tissue without respect to cell heterogeneity. In reality, only a small subpopulation of migratory and invasive cells inside the primary tumor is responsible for escaping and initiating dissemination and metastasis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15524

8 Samples

Download data: GPR, TXT

(Submitter supplied) To identify gene expression profile changes upon SNRNP40 depletion, RNA-sequencing was performed on breast cancer cells transfected with siRNAs targeting SNRNP40.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) We aimed to understand the transcriptome patterns of organ-derived cancer cell isolates from MMTV-PyMT mice. Tissues from primary tumors and organs harboring distal metastases were harvested from cancer bearing female mice. Although metastatic progression from primary tumors to lung tissue is well studied in the MMTV-PyMT model, metastases to other distal organs and the significance of intratumor heterogeneity across metastases from distal organs remain unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

17 Samples

Download data: CSV

(Submitter supplied) Purpose: The goals of this study were to establish in vivo models that recapitulated the heterogeneous behavior of osteosarcoma and to develop an approach to distinguish genes expressed from tumor cells apart from those expressed from host cells in next generation sequencing (NGS) data from xenograft tumors. Methods: We used cell lines derived from two spontaneous canine osteosarcoma tumors with distinctly different biological behaviors for heterotypic in vivo modeling. more...

Organism:

Mus musculus; Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20988 GPL22673

12 Samples

Download data: TXT