Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: RNA-seq experiments of organoids lines derived from distinct mouse prostate lobes

PROVIDER: PRJNA659468 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12519055.fastq.gz	Fastqsanger.gz
	SRR12519056.fastq.gz	Fastqsanger.gz
	SRR12519057.fastq.gz	Fastqsanger.gz
	SRR12519058.fastq.gz	Fastqsanger.gz
	SRR12519059.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 25

Similar Datasets

SPOP mutation - SPOP Mutation Drives Prostate Tumorigenesis In Vivo through Coordinate Regulation of PI3K/mTOR and AR Signaling

Project description:Recurrent point mutations in SPOP define a distinct molecular subclass of prostate cancer. Here, we describe the first mouse model showing that mutant SPOP drives prostate tumorigenesis in vivo. Conditional expression of mutant SPOP in the prostate dramatically altered phenotypes in the setting of Pten loss, with early neoplastic lesions (high-grade prostatic intraepithelial neoplasia) with striking nuclear atypia, and invasive poorly differentiated carcinoma. In mouse prostate organoids, mutant SPOP drove increased proliferation and a transcriptional signature consistent with human prostate cancer. Using these models and human prostate cancer samples, we show that SPOP mutation activates both PI3K/mTOR and androgen receptor (AR) signaling, effectively uncoupling the normal negative feedback between these two pathways. Associated RNA-seq data deposited in GEO: GSE94839.

2017-03-20 | PXD005309 | Pride

Single cell atlas of epithelial and stromal cell heterogeneity by lobe and strain in the mouse prostate

Project description:Evaluating the complex interplay of cell types in the tissue microenvironment is critical to understanding the origin and progression of diseases in the prostate and potential opportunities for intervention. Mouse models are an essential tool to investigate the molecular and cell-type-specific contributions of prostate disease at an organismal level. While there are well-documented differences in the extent, timing, and nature of disease development in various genetically engineered and exposure-based mouse models in different mouse strains and prostate lobes within each mouse strain, the underlying molecular phenotypic differences in cell types across mouse strains and prostate lobes are incompletely understood.

2022-11-14 | GSE165741 | GEO

Basal-to-inflammatory transition enhances basal cell carcinoma (BCC) therapy resistance via crosstalk with a pro-inflammatory stromal niche [RNA-seq II]

Project description:The goal of these RNA-seq experiments was to determine transcriptomic gene expression changes caused by 7 days of Il1a and Osm combination treatment of mouse primary BCC tumor-derived organoids compared to PBS control

2024-07-26 | GSE273014 | GEO

RNA-Seq of MSK-PCa series of Patient Derived Organoids and Xenografts

Project description:Transcriptome profiling analysis was performed in 22 human prostate cancer organoids, 6 patient-derived xenografts (PDXs) and 7 cell lines.

2021-08-04 | GSE181374 | GEO

RNA-seq of mouse prostate basal cell organoids treated under different androgen and Wnt signaling conditions

Project description:To determine the role of Wnt and AR signaling pathway crosstalk on prostate basal stem cells, RNA-seq was performed for mouse prostate basal cell organoids treated under three conditions.

2023-06-28 | GSE220499 | GEO

Gene expression profile of Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP)

Project description:Gene expression profile of Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) reveals murine targets for preclinical development of human prostate cancer therapy In this study, we have generated an open source TRAMP microarray dataset to identify differentially expressed genes from human prostate cancer that have concordant expression in TRAMP tumors, and thereby represent lead targets for preclinical therapy development. Affymetrix Mouse 430 2.0 chips were used for microarrays of total RNA from 9 TRAMP tumors and 9 normal prostates (ventral and dorsolateral lobes). Keywords: prostate cancer, TRAMP

2008-12-31 | GSE10525 | GEO

Dissecting the Biology of Early-onset Colorectal Cancer

Project description:Contrarily to late-onset (LO) colorectal cancer (CRC), early-onset (EO) CRC incidence is increasingly growing. Several factors, such as obesity, chronic inflammation, and intestinal dysbiosis, can increase the general risk of CRC. However, little is known about the biology of EO-CRC. To evaluate whether such selective rise in the incidence of EO-CRC patients mirrors a distinct transcriptomic profile, the investigators will first dissect EO-CRC’s transcriptomic landscape. Then, the investigators will investigate the colorectal cancer stem cell (CSC) compartment by in vitro functional assays and RNA-seq analysis. Because our preliminary data indicate an increased aggressiveness of the tumor microenvironment (TME) in EO-CRC,the investigators propose to investigate the CSC niche and the interaction with the TME to dissect the molecular and cellular pathways occurring in EO-CRC. A cohort of 30 EO-CRC patients (<50 years old) will be enrolled and fully characterized. About 10 EO-CRC-derived CSCs in the form of organoids and spheroids will be generated. Since the relevant differences between CR-CSCs isolated from EO-CRC vs LO-CRC patients are still unknown, the investigators will gain information about their specific features such as clonogenic activity, tumorigenic/invasive capacity, and about differences in the mechanisms regulating their cross-talk with TME components.

| 64348 | ecrin-mdr-crc

Transcription profiling of mouse transgenic adenocarcinoma of the prostate (TRAMP)

Project description:Gene expression profile of Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) reveals murine targets for preclinical development of human prostate cancer therapy; In this study, we have generated an open source TRAMP microarray dataset to identify differentially expressed genes from human prostate cancer that have concordant expression in TRAMP tumors, and thereby represent lead targets for preclinical therapy development. Affymetrix Mouse 430 2.0 chips were used for microarrays of total RNA from 9 TRAMP tumors and 9 normal prostates (ventral and dorsolateral lobes). Experiment Overall Design: normal prostate vs. TRAMP

2009-01-14 | E-GEOD-10525 | biostudies-arrayexpress

Single cell RNA-sequencing of vehicle- and UK5099-treated mouse prostate organoids

Project description:The goal of this study was to determine how modulation of mitochondrial pyruvate metabolism regulates gene expression in a three-dimensional organoid model of mouse prostate epithelium. Organoids were treated with the small molecule UK5099, which impairs mitochondrial pyruvate uptake, and subjected to single-cell RNA-sequencing. Our analysis revealed considerable heterogeneity within prostate organoids characterized by distinct cell clusters expressing markers associated with basal, luminal and mesenchymal-like cells. UK5099 treatment led to a reduction in epithelial populations and an enrichment in mesenchymal-like cells. These findings indicate that pyruvate metabolism can modulate features of cell fate in prostate epithelium.

2022-06-24 | GSE206555 | GEO

Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics

Project description:Human iPSC-derived kidney organoids have the potential to revolutionize discovery, but assessing their consistency and reproducibility across iPSC lines, and reducing the generation of off-target cells remain an open challenge. Here, we used single cell RNA-Seq (scRNA-Seq) to profile 450,118 cells to show that organoid composition and development are comparable to human fetal and adult kidneys. Although cell classes were largely reproducible across iPSC lines, time points, protocols, and replicates, cell proportions were variable between different iPSC lines. Off-target cell proportions were the most variable. Prolonged in vitro culture did not alter cell types, but organoid transplantation under the mouse kidney capsule diminished off-target cells. Our work shows how scRNA-seq can help score organoids for reproducibility, faithfulness and quality, that kidney organoids derived from different iPSC lines are comparable surrogates for human kidney, and that transplantation enhances their formation by diminishing off-target cells.

2019-11-04 | GSE136314 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data