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GSE34042
Homo sapiens
12 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The insulin-like growth factor-I (IGF-IR) and androgen (AR) receptors are important players in prostate cancer biology. Functional interactions between the IGF-I and androgen signaling pathways seem to have crucial roles in the progression of prostate cancer from early (benign) to advanced (metastatic) stages. DNA methylation is a major epigenetic alteration affecting gene expression. Hypermethylation of tumor suppressor promoters is a frequent event in human cancer, leading to inactivation and repression of specific genes. The aim of the present study was to identify the entire set of methylated genes (methylome) in a cellular model that replicates prostate cancer progression.
Publication Title
Global methylation analysis identifies PITX2 as an upstream regulator of the androgen receptor and IGF-I receptor genes in prostate cancer.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
The effect of transient transfection of a construct designed to over-express the androgen receptor (AR) variant AR-V7 on gene expression in MDA-MB-453 cells was assessed using Affymetrix Gene 2.0 ST arrays. Transfection of an AR-expressing construct or an empty construct served as controls.
Publication Title
Expression of androgen receptor splice variants in clinical breast cancers.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 41 Downloadable Samples
Illumina HiSeq 2500
Description
Liquid biopsies have demonstrated that the constitutively active androgen receptor splice variant-7 (AR-V7) associates with reduced response and overall survival (OS) from endocrine therapies in castration resistant prostate cancer (CRPC). However, these studies provide little information pertaining to AR-V7 biology and expression in prostate cancer (PC) tissue. Following generation and validation of a novel AR-V7 antibody for immunohistochemistry (IHC); nuclear AR-V7 protein expression was determined for 358 primary prostate samples (358 patients) and 293 metastatic biopsies (194 patients). Associations with disease progression, nuclear AR full length (AR-FL) expression, response to abiraterone and/or enzalutamide, and gene signatures (from three independent cohorts) was determined. Overall design: RNA sequencing of metastases from individuals with castration resistant prostate cancer (CRPC) using Illumina HiSeq 2500.
Publication Title
Androgen receptor splice variant-7 expression emerges with castration resistance in prostate cancer.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 22 Downloadable Samples
- NextSeq 500
Description
Alterations in gene expression following fatty acid synthase inhibtion were evaluated in androgen sensitive LNCaP cells and castration resistant 22Rv1 and LNCaP-95 cells. Cell were exposed to 2 concentrations (0.1 and 0.5 uM) of FASN inhibitor IPI-9119 or DMSO for 6 days. Overall design: Differential gene expression anlaysis in 3 prostate cancer cell lines treated with FASN inhibitor IPI-9119
Publication Title
Inhibition of de novo lipogenesis targets androgen receptor signaling in castration-resistant prostate cancer.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 250 Downloadable Samples
- Illumina HiSeq 2500, Ion Torrent Proton
Description
The goal of this study is to compare transcriptional profiles of regulatory T cells and conventional CD4 T cells in human breast cancer to regulatory T cells and conventional CD4 T cells in normal breast parenchyma and in peripheral blood. Overall design: RNA sequencing of 2 different cell types in 3 different tissues
Publication Title
Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 5 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The PI3K/Akt signaling pathway impacts various aspects of CD8 T cell homeostasis, such as effect versus memory cell differentiation, during viral infection. We used microarrays to determine which downstream molecules were affected and what other signaling pathways were interconnected with the Akt pathway by constitutive activation of Akt in LCMV-infected CD8 T cells.
Publication Title
Signal integration by Akt regulates CD8 T cell effector and memory differentiation.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
- NextSeq500
Description
Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated prior to biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from over 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas. Overall design: 3 replicates from GM12878 and HL-60 cell lines collected for differential gene expression analysis.
Publication Title
Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
The nipple is an example of specialized epidermis. The unique epidermal stratification and gene expression is induced and maintained by developmental distinct fibroblast populations.
Publication Title
Estrogen modulates mesenchyme-epidermis interactions in the adult nipple.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
CD133 is expressed by a subpopulation of human fetal hair follicle placode cells during early hair development. Its expression, which is gradually lost as the placode matures, correlates with early morphogenesis.
Publication Title
CD133 expression correlates with membrane beta-catenin and E-cadherin loss from human hair follicle placodes during morphogenesis.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
We report the differential gene expression differences between control and Ovol2-deficent newborn keratinocytes Overall design: Two control and two Ovol2-deficent samples were isolated
Publication Title
An Ovol2-Zeb1 transcriptional circuit regulates epithelial directional migration and proliferation.
Sample Metadata Fields
Specimen part, Subject
View Samples