GEO DataSets

(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) Treatment of triple-negative breast cancer has been challenging and paclitaxel resistance is one of the major obstacles to the better prognosis. Misregulation of alternative splicing (AS) may contribute to tumor progression and chemotherapy resistance. Human AS factor TRA2 has two separate gene paralogs encoding TRA2A and TRA2B proteins. TRA2B is associated with cancer cell survival and therapeutic sensitivity. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL17586 GPL17585

18 Samples

Download data: CEL, CHP

(Submitter supplied) We provide a novel gene fusion (ETV6-IgH) involving a truncation of ETV6 and leading to haploinsuffiency of ETV6 expression. ETV6-IgH is a new potential surrogate marker of PCNSL with favorable prognosis

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) MAFK is one of small Maf transcripton factor famiy molecules. We found MAFK is highly expressed in several cancer cells and related to tumorigenesis. Then, we established MAFK stable cell lines using NMuMG cells (mouse mammary glad epithelium) and used microarrays to examine gene expression alteration.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

3 Samples

Download data: CEL

(Submitter supplied) Background: Genomic analyses of hundreds of prostate tumors have defined a diverse landscape of mutations and genome rearrangements, but the transcriptomic effect of this complexity is less well understood, particularly at the individual tumor level. We selected a cohort of 25 high-risk prostate tumors, representing the lethal phenotype, and applied deep RNA-sequencing and matched whole genome sequencing, followed by detailed molecular characterization. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array; Genome variation profiling by genome tiling array

Platforms:

GPL10123 GPL10152

28 Samples

Download data: TXT

(Submitter supplied) Next generation sequencing was used to identify Notch mutations in a large collection of diverse solid tumors. NOTCH1 and NOTCH2 rearrangements leading to constitutive receptor activation were confined to triple negative breast cancers (TNBC, 6 of 66 tumors). TNBC cell lines with NOTCH1 rearrangements associated with high levels of activated NOTCH1 (N1-ICD) were sensitive to the gamma-secretase inhibitor (GSI) MRK-003, both alone and in combination with pacitaxel, in vitro and in vivo, whereas cell lines with NOTCH2 rearrangements were resistant to GSI. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

27 Samples

Download data: TXT

(Submitter supplied) mRNA profiling data for 58 breast cancer cell lines at baseline

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10379

58 Samples

Download data: CEL

(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) Triple-negative breast cancers (TNBCs) are a heterogeneous set of tumors defined by an absence of actionable therapeutic targets (ER, PR, and HER-2). Microdissected normal ductal epithelium from healthy volunteers represents a novel comparator to reveal insights into TNBC heterogeneity and to inform drug development. Using RNA-sequencing data from our institution and The Cancer Genome Atlas (TCGA) we compared the transcriptomes of 94 TNBCs, 20 microdissected normal breast tissues from healthy volunteers from the Susan G. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9520

10 Samples

Download data: 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

Platform:

GPL18573

8 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We demostrated that ELK3-Mid51 axis in TNBCs mediate mitochondrial dynamics determines concentration of reactive oxygen species that is linked to the immune sensitivity to cytotoxicity of NK cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) We demostrated that ELK3-Mid51 axis in TNBCs mediate mitochondrial dynamics determines concentration of reactive oxygen species that is linked to the immune sensitivity to cytotoxicity of NK cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: BIGWIG

(Submitter supplied) Triple-negative breast cancer (TNBC) is an aggressive disease subtype with limited treatment options. Eribulin is a chemotherapeutic approved for the treatment of advanced breast cancer that has been shown to elicit epigenetic changes. We investigated the effect of eribulin treatment on genome-scale DNA methylation patterns in TNBC cells. Following repeated treatment, The results showed that eribulin-induced changes in DNA methylation patterns evident in persister cells. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

11 Samples

Download data: CSV, IDAT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

36 Samples

Download data

(Submitter supplied) Triple-negative breast cancer (TNBC) patients have a poor prognosis and few treatment options. Mouse models of TNBC are important for development of new therapies, however, few mouse models represent the complexity of TNBC. Here, we develop a female TNBC murine model by mimicking two common TNBC mutations with high co-occurrence: amplification of the oncogene MYC and deletion of the tumor suppressor PTEN. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

16 Samples

Download data: TXT

(Submitter supplied) Triple-negative breast cancer (TNBC) patients have a poor prognosis and few treatment options. Mouse models of TNBC are important for development of new therapies, however, few mouse models represent the complexity of TNBC. Here, we develop a female TNBC murine model by mimicking two common TNBC mutations with high co-occurrence: amplification of the oncogene MYC and deletion of the tumor suppressor PTEN. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

20 Samples

Download data: CSV

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

Organism:

Xenopus laevis

Type:

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

Platform:

GPL21248

12 Samples

Download data

(Submitter supplied) VEGFA signaling is crucial for physiological and pathological angiogenesis and hematopoiesis. Although many context-dependent signaling pathways downstream of VegfA have been uncovered, vegfa transcriptional regulation in vivo is unclear. Here, we show that ETS transcription factor Etv6 positively regulates vegfa expression during blood stem cell development through multiple transcriptional inputs. more...

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21248

6 Samples

Download data: BED