GEO DataSets

(Submitter supplied) Triple-Negative Breast Cancer (TNBC) is the most aggressive breast cancer subtype, characterized by extensive intratumoral heterogeneity, high metastasis and chemoresistance, leading to poor clinical outcomes. Despite progress, the mechanistic basis of these aggressive behaviours remains poorly understood. Using single-cell and spatial transcriptome analysis, here we discovered basal epithelial subpopulations located within the stroma that exhibit chemoresistance characteristics. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

21 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL30882

4 Samples

Download data: BIGWIG, MTX, TABULAR, TSV

(Submitter supplied) In this study, we have employed both bulk RNA- and sc-RNA-seq to investigate the transcriptional status of TNBC cells, grown as 2D or 3D cultures, prior and after development of resistance to two widely used chemotherapeutic drugs, paclitaxel and doxorubicin. Our aim was to uncover the gene expression programs that support drug tolerance in treatment-naïve cells and drug resistance in heterogeneous chemoresistant populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: BIGWIG, TABULAR

(Submitter supplied) In this study, we have employed both bulk RNA- and sc-RNA-seq to investigate the transcriptional status of TNBC cells, grown as 2D or 3D cultures, prior and after development of resistance to two widely used chemotherapeutic drugs, paclitaxel and doxorubicin. Our aim was to uncover the gene expression programs that support drug tolerance in treatment-naïve cells and drug resistance in heterogeneous chemoresistant populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30882

2 Samples

Download data: MTX, TSV

(Submitter supplied) RNA-sequencing was performed in SUM 159 parental and PTX resistant breast cancer cells in an effort to identify novel regulators of chemoresistance that could potentially be targeted in Triple Negative Breast Cancer (TNBC). The bioinformatic analysis identified numerous differentially expressed genes including several known chemoresistance markers, as well as novel genes that may play an important role in breast cancer chemoresistant cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TXT

(Submitter supplied) Experiment type: Expression profiling by microarray and RNA-seq data, Third-party re-analysis The purpose of our study is to construct breast cancer cell line BT20-specific interactome by aggregating publically available microarray or RNA-seq samples, and identify novel transcriptional regulators that control breast cancer progression. We collected 101 samples of BT20 cell line microarray or RNA-seq from 12 prior studies and our own study data, GSE120919. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing; Third-party reanalysis

Download data: TXT

(Submitter supplied) Purpose: We investigated the function of overexpressed BCL2L14-ETV6 fusion variants in triple-negative breast cancer using high-throughput mRNA sequencing (RNA-Seq) analysis in BT20 human basal-like breast cancer cell line. Methods: The BCL2L14-ETV6 fusion variants or wildtype ETV6 cDNA containing the full-length ORFs were subcloned into the lentiviral pLenti7.3 vector, and later transduced into the BT20 cell line. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

15 Samples

Download data: TXT, XLSX

(Submitter supplied) Based on the identified stress-independent cellular functions of activating transcription factor 4 (ATF4), we reported enhanced ATF4 levels in MCF10A cells treated with TGFβ1. ATF4 is overexpressed in triple negative breast cancer (TNBC) patients, but its impact on patient survival and the underlying mechanisms remain unknown. We aimed to determine ATF4 effects on breast cancer patient survival and TNBC aggressiveness, and the relationships between TGFβ and ATF4.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

20 Samples

Download data: TXT

(Submitter supplied) Triple Negative Breast Cancer (TNBC), the deadliest form of this disease, lacks a targeted therapy. TNBC tumors that fail to respond to chemotherapy are characterized by a repressed Interferon/Signal Transducer and Activator of Transcription (IFN/STAT) gene signature and are often enriched for Cancer Stem Cells (CSCs). We have found that human mammary epithelial cells that undergo an Epithelial-to-Mesenchymal Transition (EMT) following transformation acquire CSC properties. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

8 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL9052

1539 Samples

Download data

(Submitter supplied) Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intratumoral heterogeneity. To investigate the underlying biology, we conduct single-cell RNA- sequencing (scRNA-seq) of >1500 cells from six primary TNBC. Intercellular heterogeneity of gene expression programs within each tumor was variable and largely correlated with clonality of inferred genomic copy number changes, suggesting that genotype drives the gene expression phenotype of individual subpopulations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

1534 Samples

Download data: TXT

(Submitter supplied) Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intratumoral heterogeneity. To investigate the underlying biology, we conduct single-cell RNA- sequencing (scRNA-seq) of >1500 cells from six primary TNBC, together with whole exome sequencing (WES) for four of the tumors. Intercellular heterogeneity of gene expression programs within each tumor was variable and largely correlated with clonality of inferred genomic copy number changes, suggesting that genotype drives the gene expression phenotype of individual subpopulations. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

5 Samples

Download data: TXT

(Submitter supplied) Triple negative breast cancers (TNBC) are a morphologically and genetically heterogeneous group of breast cancers with uncertain prediction of biological behavior and response to therapy. The aim of our study was to analyze miRNAs expression within areas of TNBCs with different cellular morphology. We performed laser capture microdissection with PALM MicroBeam system from Zeiss and subsequent expression profiling with Affymetrix GeneChip miRNA 4.0 Arrays to identify distinct classes of miRNAs deregulated in respective tissue morphologies. more...

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL19117

74 Samples

Download data: CEL, RDATA, TXT

(Submitter supplied) NEK2 is a mitotic kinase that is upregulated and mislocalized in the nucleus of human cancer cells. NEK2 modulates expression and activity of both transcription and splicing factors in cancer cells, nevertheless whether this kinase affects transcriptome regulation genome widely and whether this activity concurs to its oncogenic activity is still unknown. Herein, by high-throughput RNA sequencing analysis of MDA-MB-231 cells transiently silenced for NEK2 we uncover an extensive modulation of triple-negative breast cancer cell transcriptome by this kinase.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) Breast cancer is a heterogeneous disease comprised of four molecular subtypes defined by whether the tumor-originating cells are luminal or basal epithelial cells. Breast cancers arising from the luminal mammary duct often express estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth receptor 2 (HER2). Tumors expressing ER and/or PR are treated with anti-hormonal therapies, while tumors overexpressing HER2 are targeted with monoclonal antibodies. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

54 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Purpose: Assess the cellular heterogeneity during the transition through partial EMT and MET in the spontaneous C3(1)-Tag breast cancer model. Methods: We performed MULTI-seq single cell RNA sequencing analysis in two different ex vivo assays: the collagen assay that models invasion and the colony formation assay that models metastatic outgrowth. Briefly, organoids were isolated from 4 different mice and either plated directly into collagen I matrix or further dissociated into clusters and plated into Matrigel. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: CSV, MTX

(Submitter supplied) To develop and validate novel multigene signatures to facilitate individualized treatment of TNBC patients By integrating expression profiles of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

198 Samples

Download data: CEL

(Submitter supplied) Background: Triple-negative breast cancer (TNBC) is a very heterogeneous disease. Several gene expression and mutation profiling approaches were used to classify it and all converged to the identification of distinct molecular subtypes, with some overlapping across different approaches. However, a standardised tool to routinely classify TNBC in the clinics and guide personalised treatment is lacking. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21185

72 Samples

Download data: TXT