GEO DataSets

(Submitter supplied) One of the factors involved in TNBC aggressiveness is HMGA1, a member of non-histone chromatin proteins. The High mobility group A1 is an architectural transcription factor which, by altering chromatin structure and interacting with transcription factors, can regulate the transcription of several genes. HMGA1 protein is defined as an oncofetal protein as it is highly expressed during the embryogenesis while its expression decreases or is absent in adults, and it is re-expressed in a variety of tumors, including breast cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

15 Samples

Download data: TXT

(Submitter supplied) we report the mapping of Fra-1 and Fra-2 binding site on MDA-MB-231 cell line genome

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

3 Samples

Download data: BED, WIG

(Submitter supplied) Emerging evidence suggests that tumor cells metastasize by co-opting stem cell transcriptional networks, although the molecular underpinnings of this process are poorly understood. Here, we show for the first time that the high mobility group A1 (HMGA1) gene drives metastatic progression in triple negative breast cancer cells (MDA-MB-231) by reprogramming cancer cells to a stem-like state. We discovered an HMGA1 signature in triple negative breast cancer cells that is highly enriched in embryonic stem cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

6 Samples

Download data: CEL

(Submitter supplied) Triple-negative breast cancer (TNBC) is defined by the absence of estrogen and progesterone receptors and human epidermal growth factor receptor 2, and is the most lethal and aggressive subtype of breast cancer. However, the genes which relate to promote tumor aggressiveness in TNBC remain unclear. In order to investigate specific genes and pathways involved in TNBC tumorigenesis, we compared genes differentially expressed between 3D cultures (3DC) or tumor xenograft models and control two-dimensional cultures (2DC).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL, TXT

(Submitter supplied) To understand the functional role of CTCF in the oncogenesis of HCC, we constructed lentiviruses expressing control shRNA (shCont) or shRNA agains CTCF (shCTCF) and transduced them into PLC5 cells respectively. After 24 hours, cells were cultered in puromycin containing medium (5 ug) for another 24 hours. Cells were returned to normal medium for another 48 hours before total mRNAs were corrected for whole genome gene expression array analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

2 Samples

Download data: TXT

(Submitter supplied) FoxM1 is an oncogenic transcription factor that has been linked to the genesis and progression of cancer. FoxM1 not only upregulates cell proliferation and survival genes, but also represses tumor suppressor genes according to our prior study. This ChIP-Seq is a part of our endeveavor to creat a map of the FoxM1 occupied chromatin area in order to better understand the FoxM1 role in tumorigenesis. We present the results of a high-throughput profile of Chromatine alteration in mammalian cells using ChIP-Seq. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: BED, BW, NARROWPEAK

(Submitter supplied) Activation of the tyrosine kinase c-Src promotes breast cancer progression and poor outcome, yet the underlying mechanisms are incompletely understood. Here, we show that deleting c-Src abrogates the activity of Forkhead Box M1 (FOXM1), a master transcriptional regulator of the cell cycle, in a genetically engineered model mimicking the Luminal B molecular subtype of breast cancer. By phosphorylating it on two tyrosine residues, c-Src stimulates the nuclear localization of FOXM1 and the expression of its target genes, including key regulators of G2-M cell cycle progression as well as c-Src itself. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: XLS

(Submitter supplied) The multitasking ProMyelocytic Leukemia (PML) protein, which was originally recognized as tumor suppressive factor, is commonly lost in primary breast cancer tissue samples. However, PML’s role in breast cancer is still debated, as high PML levels reportedly correlate with cancer cell pro-survival activity and poor patient prognosis in a subset of breast cancer types. To study the molecular mechanisms underlying the involvement of PML in cell proliferation and self-renewal pathways in breast cancer, a transgene expressing PMLIV upon doxycycline treatment was stably integrated in MDA-MB-231 cells (tetPMLIV MDA-MB-231 cells), a claudin-low, triple negative, aggressive breast cancer cell line. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

8 Samples

Download data: CEL, CHP

(Submitter supplied) To identify potential PTTG1-targeted genes, total RNA from PTTG1+/+ and PTTG1-/- HCT 116 cells was isolated using the RNeasy Kit (Qiagen) and analyzed using Illumina microarrays (HumanHT-12_V4). Raw data were processed according to the manufacturer’s standard procedure and further analyzed using Partek 6.5.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

6 Samples

Download data: TXT

(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) FOXM1 transcription factor is an oncogene and a crucial regulator of cancer chemoresistance. Existing pharmacological FOXM1 inhibitors attenuate resistance of cancer cells to treatment but exhibit insufficient specificity. We performed in silico screening of small molecules from NIH LINCS database to identify STL427944 compound that suppresses FOXM1 through a novel two-step mechanism. STL427944 treatment induces relocalization of nuclear FOXM1 protein to cytoplasm, where it is subsequently degraded in an autophagosome-dependent manner. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: TXT

(Submitter supplied) Analysis of MDA-MB-231 breast cancer cells depleted for High Mobility Group A1 (HMGA1) using siRNA. HMGA1 is involved in invasion and metastasis in breast cancer cells. Results identify the specific transcriptional program induced by HMGA1 in highly metastatic breast cancer cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) By chromatine-immunoprecipitating (ChIP) using the mammary epithelial cell line HMLE with a Doxycyclin-inducible overexpression of SOX4 we determined various histone modifications and presence of the POL2 polymerase in presence and absence of overexpressed SOX4.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: BW

(Submitter supplied) Through RNA-sequencing we analysed the differentially expressed genes upon inducible activation of SOX4.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: DIFF

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. The experiments are described in 2 papers: PMID 30137431 and PMID 30507376

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

50 Samples

Download data: BIGWIG, BW

(Submitter supplied) In order to identify genes co-bound by SOX4 and SMAD3 in the context of breast cancer, different breast cell lines (HMLEs, MDA-MB-231 or HCC-1954) were used. Due to low endogenous expression levels for SOX4 in HMLEs in untreated conditions, doxycycline-dependent SOX4 overexpression was obtained by transducing HMLE cells with pIINDUCER21-SOX4 vector..Cells were plated and SOX4 and SMAD3 chromatine-immunoprecipitation was performed in untreated conditions, TGF-beta (2.5ng/ml), doxycycline (0.5ug/ml) or both as indicated. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

25 Samples

Download data: BIGWIG, BW

(Submitter supplied) In order to identify SOX4- and TGF-beta dependent genes, human mammary epithelial cells (HMLEs) were transduced with shRNA scrambled (control) or shRNA targeting SOX4 (TRCN0000018213, Sigma Aldrich, St. Louis, MS) and selected with puromycin for at least 2 weeks. SOX4 knockdown was confirmed by qRTPCR and western blotting. Cells were plated in 6 well plates and either left untreated or treated with TGF-beta (2.5ng/ml) for 16 hours in biological duplicate (different passages). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) The expression of the transcription factor SOX4 is increased in many human cancers, however, the pro-oncogenic capacity of SOX4 can vary greatly depending on the tumor-type. Both the contextual nature and the mechanisms underlying the pro-oncogenic SOX4 response remain unexplored. Here, we demonstrate that in mammary tumorigenesis, the SOX4 transcriptional network is dictated by the epigenome and is enriched for pro-angiogenic processes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

11 Samples

Download data: TXT

(Submitter supplied) Analysis of the transcriptome of mouse models of prostate cancer to assemble a mouse prostate cancer interactome. To assemble the mouse prostate cancer interactome, we collected 13 distinct mice or genetically-engineered mouse models (GEMMs), which together represent the full spectrum of prostate cancer phenotypes including: normal epithelium (i.e., wild-type), low-grade PIN (i.e., Nkx3.1 and APT), high-grade PIN and adenocarcinoma (i.e., APT-P; APC; Myc; NP; Erg-P; and NP53), castration-resistant prostate cancer (i.e., NP-AI), and metastatic prostate cancer (i.e., NPB; NPK; and TRAMP). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

384 Samples

Download data: TXT

(Submitter supplied) To investigate the effect of HMGA1 in pancreatic cancer. Here we established E3LZ10.7 cell lines in which HMGA1 has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT