GEO DataSets

(Submitter supplied) Cancer stem cells (CSCs) are proposed to be responsible for metastatic dissemination and clinical relapse in a variety of cancers. Analogies between CSCs and normal tissue stem cells (SC) has led to the notion that CSCs often co-opt the normal SC program of their tissue-of-origin. The cell-biological program termed epithelial-mesenchymal transition (EMT) has been found to encourage entrance of normal and neoplastic mammary cells into the corresponding SC states. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL17021

4 Samples

Download data: BED

(Submitter supplied) Elf5 (or ESE-2) is an ETS transcription factor that is abundantly expressed in the mammary epithelium, where it plays a critical role in dictating cell fate and lineage choices. These changes are in part mediated by alterations in the expression and activity of critical components of the Jak/Stat pathway. While the biological function of Elf5 in mammary gland development has been well characterized, its role in breast cancer remains to be elucidated. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

10 Samples

Download data: TXT

(Submitter supplied) Elf5 induced transcriptional changes in MDA-MB-231 origin, control (mut Elf5) vs WT ELF5

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

6 Samples

Download data: TXT

(Submitter supplied) Elf5 induced transcriptional changes in high lung metastasis subline LM2 (MDA-MB-231 origin), control (GFP) vs ELF5

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

4 Samples

Download data: TXT

(Submitter supplied) We developed conditional knockout mice where the transcription factor Elf5 (also called ESE-2) is deleted in the mammary glands. Loss of Elf5 results in block in alveologenesis and epithelial differentiation defects. Mammary gland samples from Elf5 knockout and wild type animals were analyzed for global transcriptome changes.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

20 Samples

Download data: TXT

(Submitter supplied) MaSC, Luminal progenitor enriched subpopulations were isolated from virgin and pregnant mice based on using both surface marker or internal reporter transgene (GFP) expression. (Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035), and the transcirptome profiles were determined and compared.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

14 Samples

Download data: TXT

(Submitter supplied) MaSC, luminal progenitor enriched subpopulations and total MECs as well, were isolated from both wild type and ∆Np63 KO heterozygous mouse and the transcriptome profiles were determined and compared.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

6 Samples

Download data: TXT

(Submitter supplied) We report the ChIP-Seq results of SNAI2 in several different conditions which include: SNAI2 binding in both control and SNAI2 knockdown cells to demonstrate specificity of the binding. SNAI2 ChIP-Seq was also performed in SNAI2 or control LACZ overexpressing cells cultured in growth medium as well as LACZ or SNAI2 overexpressing cells in differentiation medium.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: TXT

(Submitter supplied) 1. Keratinocytes infected with retroviruses expressing control or SNAI2 shRNAs were cultured in growth medium and Affymetrix HG-U133 plus 2.0 arrays were used to determine global gene expression profiles. 2. Keratinocytes infected with retroviruses overexpressing LACZ or SNAI2 were cultured in growth medium and Affymetrix HG-U133 plus 2.0 arrays were used to determine global gene expression profiles.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL, CHP

(Submitter supplied) Tumor-initiating cells (TICs) exist in breast cancer and are thought to be the cause of tumor initiation, progression, and relapse. In these processes, proteases play an important role. Additionally, conditions of the tumor milieu, including hypoxic nutrient-deprived as well as normoxic nutrient-rich environments, influence the tumor-promoting actions of neoplastic cells. Therefore, we investigated the role of proteases in TICs and their response to different environments by means of a generated immortalized TIC line. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

12 Samples

Download data: TXT

(Submitter supplied) This experiment shows differential expression of genes in the luminal, basal and stromal subpopulations from SNAI2+/+ and SNAI2 LacZ/LacZ mammary epithelial cells.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

24 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL10481 GPL17784

21 Samples

Download data

(Submitter supplied) Alterations that perturb differentiation and cell state transitions can lead to defects in development, function and the genesis of cancer. Studying cellular plasticity at high resolution and in real time has proven difficult using existing methods. Here, we use a quantitative approach to gain insights into cell state dynamics of normal mammary epithelial cells (MECs) and validate the model's predictions in vivo. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10481

18 Samples

Download data

(Submitter supplied) Gene expression data of MCF10A cell subpopulations: luminal, basal and luminal.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17784

3 Samples

Download data: TXT

(Submitter supplied) Purpose: The aim of this study is to explore histone modification in four basal cell populations defined by Lgr5 and Tspan8 expression taken from adult mouse mammary glands using chromatin immunoprecipitation sequencing (ChIP-seq). Methods: The ChIP DNA samples were prepared and indexed for Ilumina sequencing using the TruSeq DNA sample Prep Kit (Ilumina) as per manufacturer's instruction. The library was quantified using the Agilent Tapestation and the Qubit's RNA assay kit for Qubit 2.0 Fluorometer (Life Technologies). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

24 Samples

Download data: TXT

(Submitter supplied) Purpose: The aim of this study is to identify genes that are differentially expressed in the different basal cell populations defined by Lgr5 and Tspan8 (T8) expression from adult mouse mammary glands. Methods: Total RNA was extracted from sorted basal populations defined by Lgr5 and Tspan8 expression from the mammary glands of 10-week-old Lgr5-GFP-IRES-creERT2 female mice. Total RNA (50 ng) for each of the two biological replicates was used to generate libraries for whole-transcriptome analysis following Illumina's TruSeq RNA v2 sample preparation protocol. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: TXT

(Submitter supplied) The aim of this study is to identify genes that are differentially expressed in basal cell populations with different levels of Lgr5 gene expression. Samples were isolated from adult mouse mammary glands.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

9 Samples

Download data: TXT

(Submitter supplied) This experiment shows RNA-Seq gene expression profiles of Wild Type and Slug/Snai2-null luminal, basal, and stromal mammary cell populations from young (3 mo) and aged (12 mo) mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

26 Samples

Download data: TXT

(Submitter supplied) Expression of the EMT-inducing transcription factor Snail is enhanced in different human cancers. To investigate the in vivo role of Snail during progression of epithelial cancer, we used a mouse model with skin-specific overexpression of Snail. Snail transgenic mice spontaneously developed distinct histological subtypes of skin cancer, such as basal cell carcinoma, squamous cell carcinoma and sebaceous gland carcinoma. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

8 Samples

Download data: CEL