GEO DataSets

(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:

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:

GPL11154

15 Samples

Download data: BED, BW, TXT

(Submitter supplied) To obtain more information about the lymph node metastasis of breast cancer cells, we selected the matched primary breast cancer (PC), positive lymph nodes (PL), and negative lymph nodes (NL) of the same patient to perform integrated analysis. The PC, PL, NL samples were analysed with single-cell RNA sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

3 Samples

Download data: TXT

(Submitter supplied) To obtain more information about the lymph node metastasis of breast cancer cells, we selected the matched positive lymph nodes (PL), and negative lymph nodes (NL) of the same patient to perform integrated analysis. The PL, NL samples were analysed with single-cell ATAC sequencing.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: BED, MTX, TSV

(Submitter supplied) The central nervous system (CNS) is a common site of metastatic disease in patients with breast cancer and has few therapeutic options with dismal outcomes. The purpose of our study was to identify common and rare events that underlie breast cancer CNS metastasis. We performed deep genomic profiling, which integrated gene copy number, gene expression and DNA methylation datasets on a collection of breast brain metastases. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

55 Samples

Download data: TXT

(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) 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

Platform:

GPL16791

12 Samples

Download data: BEDGRAPH

(Submitter supplied) RNA-seq experiments revealed an A-fat and GF-fat selective gene expression signature, with 126 genes up-regulated in abdominal preadipocytes and 90 genes up-regulated in GF cells. Assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) identified almost 10-times more A-specific chromatin-accessible regions. Using a combined analysis of ATAC-seq and global gene expression data, we identified 74 of the 126 abdominal-specific genes (59%) with A-specific accessible chromatin sites within 200kb of the transcription start site (TSS). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: BEDGRAPH

(Submitter supplied) RNA-seq experiments revealed an A-fat and GF-fat selective gene expression signature, with 126 genes up-regulated in abdominal preadipocytes and 90 genes up-regulated in GF cells. Assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) identified almost 10-times more A-specific chromatin-accessible regions. Using a combined analysis of ATAC-seq and global gene expression data, we identified 74 of the 126 abdominal-specific genes (59%) with A-specific accessible chromatin sites within 200kb of the transcription start site (TSS). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

102 Samples

Download data

(Submitter supplied) Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

52 Samples

Download data: BW

(Submitter supplied) Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

50 Samples

Download data: BW

(Submitter supplied) we reported the development of an accurate, easy-to-use and scalable system (SNuBar) for multiplexing single cell ATAC or multi-omics (ATAC&RNA) assays, and applied this method to multiplex therapy combinations in a lung cancer mouse model and macro-spatial regions of normal breast tissues and samples.

Organism:

Homo sapiens; Mus musculus

Type:

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

6 related Platforms

15 Samples

Download data: BED, CSV, MTX, TBI, TSV, TXT

(Submitter supplied) Cardiac pacemaker cells (PCs) in the sinoatrial node (SAN) have a distinct gene expression program that allows them to fire automatically and initiate the heartbeat. Although critical SAN transcription factors, including Isl1, have been identified, the cis-regulatory architecture that governs PC-specific gene expression is not understood, and discrete enhancers required for gene regulation in the SAN have not been identified. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL21103

13 Samples

Download data: BW, TXT

(Submitter supplied) The ability to predict metastatic potential is of clinical and biological importance. Numerous metastasis/relapse predictors exist for breast cancer patients; however, what is less well established is whether predicting metastasis to specific organs sites is feasible. In this study we sought to determine: 1) the degree to which gene signatures vary across tumors and their metastases, 2) if genomic intrinsic subtypes associate with particular organs of relapse, and 3) if other genomic signatures can predict spread to specific organs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

7 related Platforms

414 Samples

Download data

(Submitter supplied) Enhancer variation has been proposed as a major cause of cancer heterogeneity – however, mechanisms driving patient-specific enhancer cartographies remain unclear. Here we applied microscale histone modification profiling to delineate the landscape of enhancers in primary gastric adenocarcinoma, analyzing 132 epigenomic profiles of primary tumors, normal tissues, and cell lines

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

72 Samples

Download data: BW

(Submitter supplied) Multiple convergent pathways resulting in inhibition of the transcription factor EBF1 is a major cause of TERT upregulation.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL20301

36 Samples

Download data: BW, TXT, XLS, XLSX

(Submitter supplied) Multiple convergent pathways resulting in inhibition of the transcription factor EBF1 is a major cause of TERT upregulation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

3 Samples

Download data: TXT