GEO DataSets

(Submitter supplied) We report the generation of a preclinical IBC patient-derived xenograft (PDX)-derived ex vivo tumor tissue model and show that it closely replicates the tissue architecture of the original PDX tumor harvested from mice and show that its genetic signature highly correlates with that of the original tumor. We used microarrays to evaluate the robustness and reproducibility of the method used to generate the ex vivo tumor tissue model and confirm its ability to recapitulate the essential features of the original tumor.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

8 Samples

Download data: CEL

(Submitter supplied) Inflammatory breast cancer (IBC) is the most aggressive type of advanced breast cancer and is associated with a poor prognosis. We have developed a new model of IBC derivated from the pleural effusion of a 49-year-old woman with metastatic secondary IBC. FC-IBC02 tumor cells were isolated from the pleural effusion and cultured under non-adherent conditions, resulting in the formation of spheroids or mammospheres. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

14 Samples

Download data: CEL

(Submitter supplied) We used the Human Transcriptome Array 2.0 expression data to examine quality control, reproducibility, and insights on differential gene expression inflammatory breast cancer biopsy specimens prior to systemic treatment.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17585

10 Samples

Download data: CEL, CHP

(Submitter supplied) Non-gestational choriocarcinoma (NGC) is a rare subtype of malignant germ cell tumor. We established a patient-derived xenograft (PDX) model using tumor tissue from an 18-year-old patient with NGC. Then, we performed mRNA-seq analysis using the fresh-frozen tissues of the original tumor and the PDX model.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

2 Samples

Download data: TXT

(Submitter supplied) We have analyzed the gene expression-based consensus molecular subtypes of colorectal cancer. These samples represent a subset of the total series analyzed.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

174 Samples

Download data: CEL, CHP

(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) EGFR Is a Master Switch Between Immunosuppressive and Immunoactive Tumor Microenvironment in Inflammatory Breast Cancer

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: TXT

(Submitter supplied) Dysregulated choline metabolism is a well-known feature of breast cancer, but the underlying mechanisms are not fully understood. In this study, the metabolomic and transcriptomic characteristics of a large panel of human breast cancer xenograft models were mapped, with focus on choline metabolism. Methods: Tumor specimens from 34 patient-derived xenograft models were collected and divided in two. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

30 Samples

Download data: TXT

(Submitter supplied) The VEGF targeted antiangiogenic drug bevacizumab has shown varying results in clinical trials of breast cancer. Identifying robust biomarkers for selecting patients that may benefit from bevacizumab treatment and for monitoring of response is important for the future use of this drug. Two established xenograft models representing basal-like and luminal-like breast cancer were used to study bevacizumab treatment response on the metabolic and gene expression levels. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

60 Samples

Download data: TXT

(Submitter supplied) Methylation profiles of preclinical ETMR models were generated and compared to reference primary human tumors to determine the molecular fidelity of the preclinical model systems.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL21145

6 Samples

Download data: IDAT

(Submitter supplied) Gene expression data from this ETMR cell line was compared with gene expression data from primary ETMR tumors to search for potential drug targets in ETMR tumors.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

1 Sample

Download data: CEL

(Submitter supplied) Purpose: Transcriptome profiling (RNA-seq) of a novel human Inflammatory Breast Cancer cell line A3250 in comparison to SUM149 and MDA-MB-231 Inflammatory Breast Cancer (IBC) is the most aggressive form of breast cancer with distinct clinical and histopathological features, but understanding of the unique aspects of IBC biology lags far behind that of other breast cancers. We describe a novel triple-negative IBC cell line, A3250, that recapitulates key features of human IBC in a mouse xenograft model.The purpose of this study was to compare differences in gene expression between A3250 IBC, MDA-MB-231 non-IBC and SUM149 IBC that does not present with typical clinical sympotms of IBC in a mouse model, with the goal of identifying unique molecular features for this unique type of breast cancer Results: RNA-Seq analysis identified expression profile characteristic for the novel A3250 IBC cell line, compared to SUM149 IBC and MDA-MB-231 non-IBC.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: TXT

(Submitter supplied) Inflammatory Breast Cancer (IBC) is the most aggressive form of breast cancer, but understanding of the unique aspects of IBC biology lags far behind that of other breast cancers. One of the key barriers in advancing understanding of the molecular determinants of IBC has been the lack of adequate models for this disease that presents with distinct clinical and histopathological features. We describe here a novel human triple-negative IBC cell line, A3250, that recapitulates key features of human IBC in a mouse orthotopic model including skin erythema, diffuse tumor growth, high stroma to tumor ratio, dermal lymphatic invasion, and extensive lymph node and distant metastases. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: CSV

(Submitter supplied) Purpose: Transcriptome profiling (RNA-seq) of a novel human Inflammatory Breast Cancer cell line A3250 and its xenograft tumors Methods: A3250 tumor cells were maintained as adherent cultures in standard tissue culture dishes, in high-glucose DMEM supplemented with 4 mM L-glutamine, 10% FBS, and 1X antibiotics (100 U/ml penicillin, 100 U/ml streptomycin) Tumor cells cultured in vitro were harvested for RNA-Seq analysis at 80% confluency. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL6480 GPL16895

90 Samples

Download data: GPR, TXT

(Submitter supplied) Inflammatory breast cancer (IBC) is a unique clinical entity characterized by rapid onset of erythema and swelling of the breast often without an obvious breast mass. Many studies have examined and compared gene expression between IBC and non-IBC (nIBC), repeatedly finding clusters associated with receptor subtype, but no consistent gene signature associated with IBC has been validated. Here we examined microdissected IBC tumor cells compared to microdissected nIBC tumor cells matched based on estrogen and HER-2/neu receptor status.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL16895

45 Samples

Download data: GPR

(Submitter supplied) Inflammatory breast cancer (IBC) is a unique clinical entity characterized by rapid onset of erythema and swelling of the breast often without an obvious breast mass. Many studies have examined and compared gene expression between IBC and non-IBC (nIBC), repeatedly finding clusters associated with receptor subtype, but no consistent gene signature associated with IBC has been validated. Here we examined microdissected IBC tumor cells compared to microdissected nIBC tumor cells matched based on estrogen and HER-2/neu receptor status.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

45 Samples

Download data: TXT

(Submitter supplied) Breast cancer is a heterogeneous collection of disease arising from the breast with distinct molecular and phenotypic features. Certain subsets of patients have tumors that are particularly difficult-to-treat, which include triple-negative breast cancer (TNBC), metastatic/recurrent disease and rare histological variants. To delineate the underlying biology and identify therapeutic candidates for these patients, a series of 37 breast cancer patient-derived xenografts (PDX) from both chemo-naïve and pre-treated specimens was generated from 81 transplant attempts. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

66 Samples

Download data: TXT

(Submitter supplied) To demonstrate the versatility of parallel-factor ChIP-seq, we applied our method to the analysis of ER binding in five patient-derived xenograft (PDX) samples.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: NARROWPEAK