GEO DataSets

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL570

19 Samples

Download data: BED, BW, CEL

(Submitter supplied) During cancer progression, carcinoma cells encounter a variety of cytotoxic stresses such as hypoxia, nutrient deprivation, and low pH as a result of inadequate vascularization. To maintain survival and growth in the face of these physiologic stressors, a set of adaptive response pathways are induced. One adaptive pathway well studied in other contexts is the unfolded protein response (UPR), of which XBP1 is an important component. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) We report the application of ChIP-seq, which combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing, to map genome-wide XBP1 binding sites in different breast cancer cell lines. We showed that HIF1α motif was enriched in XBP1 binding sites in triple negative breast cancer (TNBC) cell lines, but not enriched in ER positive breast cancer cell line. We also demonstrated that different breast cancer cell lines of the same sub-type had similar XBP1 binding sites, whereas different breast cancer sub-types had majorly different XBP1 binding sites. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

11 Samples

Download data: BED, BW

(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) Human X-box binding protein-1 (XBP1) is an alternatively spliced transcription factor that participates in the unfolded protein response (UPR), a stress signaling pathway that allows cells to survive the accumulation of unfolded proteins in the endoplasmic reticulum lumen. We have previously demonstrated that XBP1 expression is increased in antiestrogen-resistant breast cancer cell lines, and is co-expressed with estrogen receptor alpha (ER) in breast tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2861

Platform:

GPL96

6 Samples

Download data: CEL, CHP

Analysis of MCF7 breast cancer (BC) cells overexpressing spliced X-box binding protein-1 (XBP1), a transcription factor that participates in the unfolded protein response (UPR). Results provide insight into the role of XBP1 and the UPR in estrogen and antiestrogen responsiveness in breast cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 protocol sets

Platform:

GPL96

Series:

GSE8562

6 Samples

Download data: CEL, CHP

(Submitter supplied) Subpopulations of MDA-MB-231 that exhibit different metastatic tropisms when injected into immuno-deficient mice. Also, a cohort of primary breast cancers surgically resected at the Memorial Sloan-Kettering Cancer Center (MSKCC). Keywords = Breast cancer Keywords = lung metastasis Keywords: parallel sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

121 Samples

Download data: CEL, EXP

(Submitter supplied) We used microarray to indentify KMO-regulated genes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

2 Samples

Download data: CEL

(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) We assessed the impact of intestinal epithelial XBP1 in coordinating epithelial DNA damage responses. As our data revealed that low XBP1 activity in the context of chronic DNA damage is associated with both reduced p53 pathway activity and formation of tumors with metastaic potential in-vivo, we performed RNA sequencing of intestinal organoids (H2b/Xbp1fl/fl, H2bΔIEC, H2b/Xbp1ΔIEC, H2b/p53∆IEC) to identify a transcriptional program downstream of p53 that drives the tumorigenic in-vivo phenotype.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

15 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) Whole transcriptome sequencing was performed to identify ncRNA transcriptome in two human TNBC cell lines under normoxia and hypoxia

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Triple Negative Breast Cancer (TNBC) is an aggressive subtype of breast cancer characterized by the absence of estrogen receptor alpha, progesterone receptor, and human epidermal growth factor receptor 2 (HER2). These receptors are well characterized and often serve as targets in breast cancer treatment. As a result, TNBCs are difficult to treat and have a high propensity to metastasize to distant organs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: XLSX

(Submitter supplied) ID8-based ovarian tumors were developed for 3 weeks in wild type (WT, N=3) or conditional knockout mice selectively deleting XBP1 in CD11c positive cells (KO, N=3). Tumor-associated DCs were independently sorted via FACS and used for transcriptional profiling.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: CSV, TXT

(Submitter supplied) Triple Negative Breast Cancer (TNBC) has been considered an aggressive and complex subtype of breast cancer. Current biomarkers used in breast cancer treatment are highly dependent on targeting ER, PR, or HER2 in clinical practice, which results in ttreatment failure and disease recurrence continue to be clinically challenging. In this regards, there is still a crucial need for improvement of TNBC treatment by discovery of effective biomarkers that can be easily translated to the clinics and possible targets as prognosis and novel therapies. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18649

55 Samples

Download data: TXT

(Submitter supplied) Identification of the BCL11A-regulated transcriptome and spliceosome and determination of MBNL1-dependent splicing changes by RNA-Seq

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

11 Samples

Download data: XLSX

(Submitter supplied) To define transcriptional dependencies of TNBCs, we identified transcription factors highly and specifically expressed in primary TNBCs and tested their requirement for cell growth in a panel of breast cancer cell lines. We found that EN1 is overexpressed in TNBCs and its downregulation preferentially and significantly reduces cellular viability and tumorigenicity in TNBC cell lines. Based on RNA-seq and ChIPseq we found that EN1 regulates genes involved in angiogenesis, neurogenesis, and axon guidance in breast cancer cells. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

89 Samples

Download data: BED, CSV

(Submitter supplied) Triple negative breast cancer (TNBC) has poor prognostic outcome compared to other types of breast cancer1. At present the molecular and cellular mechanisms underlying TNBC pathology are not well understood1. Here we report that the transcription factor BCL11A is overexpressed in TNBC including basal-like breast cancer (BLBC) and that its genomic locus is amplified in up to 38% of BLBC tumours. BCL11A overexpression in immortalised human breast epithelial cells promotes tumour formation in xenograft models, whereas knockdown of BCL11A in TNBC cell lines suppresses their tumourigenic potential. In the DMBA-induced mouse mammary tumour model, Bcl11a is found to be essential for tumourigenesis since deletion of Bcl11a before DMBA treatment substantially decreases tumour formation, even in p53-null cells, and inactivation of Bcl11a in established tumours causes their regression. At the cellular level, BCL11A overexpression enhances clonogenicity in vitro whereas its deletion in the mouse causes a reduction in the number of mammary epithelial stem and progenitor cells. Thus, BCL11A has an important role in the genesis of TNBC and in normal mammary epithelial cells. This study highlights the importance of further investigation of BCL11A in breast cancer diagnosis and targeted therapies.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platforms:

GPL10904 GPL18752

7 Samples

Download data: TXT

(Submitter supplied) STAT1 and IRF1 are essential effectors of the type I and II interferon (IFN) pathways. Here, we report that the oncogenic MUC1-C protein is necessary for inducing chromatin accessibility and activation of the STAT1 and IRF1 genes in triple-negative breast cancer (TNBC) cells. Our results demonstrate that MUC1-C activates the PBRM1 subunit of the SWI/SNF PBAF chromatin remodeling complex and forms a nuclear complex with PBRM1. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data