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RNA sequencing of wildtype, PTEN single knockout (SKO), and PTEN Rb1 double knockout (DKO) mouse prostate organoids

ABSTRACT: RNA sequencing of wildtype, PTEN single knockout (SKO), and PTEN Rb1 double knockout (DKO) mouse prostate organoids

PROVIDER: PRJNA912598 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22746487.fastq.gz	Fastqsanger.gz
	SRR22746488.fastq.gz	Fastqsanger.gz
	SRR22746489.fastq.gz	Fastqsanger.gz
	SRR22746490.fastq.gz	Fastqsanger.gz
	SRR22746491.fastq.gz	Fastqsanger.gz

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RNA sequencing of wildtype, PTEN single knockout (SKO), and PTEN;Rb1 double knockout (DKO) mouse prostate organoids

Project description:The goal of this study was to perform transcriptomics on wildtype, PTEN single knockout (SKO) and PTEN;Rb1 double knockout (DKO) mouse prostate organoids. We isolated basal cells from PTEN floxed and PTEN;Rb1 floxed mouse prostates and infected with either RFP control or Cre recombinase to establish wildtype, SKO, and DKO mouse prostate organoids.

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RNA sequencing of PTEN,Rb1 double knockout (DKO) mouse prostate organoids treated with vehicle or the small molecule mitochondrial pyruvate carrier (MPC) inhibitor UK5099

Project description:The goal of this study was to determine how pharmacological inhibition of the mitochondrial pyruvate carrier (MPC) alters lineage identity in transformed prostate organoids. We isolated basal cells from PTEN,Rb1 floxed mouse prostates and infected with Cre recombinase to establish PTEN, Rb1 double knockout (DKO) mouse prostate organoids. We then treated the DKO organoids with vehicle or 10uM UK5099 for five days.

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Microarray analysis of WT, SKO, PKO and DKO liver samples

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Temporal gene expression patterns (Next Generation Sequencing) in liver tumourigenesis of hepatocyte-specific deletion of shp2 and/or pten

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to reveal dynamics of liver tumourigenesis in different mouse model and identify some key regulators that control HCC initiation or progression. We also try to define a index based on transcriptome of samples to quantify tumor development stage. Methods: mRNA profiles of wild-type (WT), hepatocyte-specific shp2 deletion (Shp2−/−) mice (SKO), hepatocyte-specific pten deletion (Pten−/−) mice (PKO), and hepatocyte-specific shp2 and pten deletion mice (DKO) were generated by deep sequencing. The sequence reads that passed quality filters were mapped to Mouse genome using STAR, and mRNA profiles were obtained using cuffdiff. Results: quanlity control of mRNA profiles showed that the data captured key features of phenotypes. Significantly changed genes, pathways, biolgocial processes, ligand and receptor, epigenetic regulators et al of SKO, PKO, DKO mice at differnet age were obtaiend. Temporal gene expression patterns during liver tumorigenesis in SKO, PKO and DKO mice were obtained. Conclusions: Our study represents the first detailed analysis of temporal transcriptomes during liver tumourigenesis, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comprehensive investigations of expression profiles.

2018-12-07 | GSE123427 | GEO

RNA sequencing of PTEN,Rb1 double knockout (DKO) mouse prostate organoids treated with vehicle or the small molecule mitochondrial pyruvate carrier (MPC) inhibitor UK5099

Project description:RNA sequencing of PTEN,Rb1 double knockout (DKO) mouse prostate organoids treated with vehicle or the small molecule mitochondrial pyruvate carrier (MPC) inhibitor UK5099

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Role of de novo DNA methyltransferases in hematopoietic stem cells (ChIP-Seq)

Project description:We investigate the dynamics for Histone marks H3K4me3 and H3K27me3 during Dnmt3a and Dnmt3b knockout in mouse hematopoietic stem cells. The term dko represents double knockout of both Dnmt3a and Dnmt3b, while the term sko denotes single knockout of Dnmt3a. The Wildtype profiles were generated in study GSE47765. Mouse hematopoietic stem cell histone methylation profiles of sko and dko mice were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000

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Transcriptome analysis of Chx10-Cre Rb1/p107 and Chx10-Cre Rb1/p107/Hells tumors

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2016-02-26 | E-GEOD-66717 | biostudies-arrayexpress

Liver tumor gene expression profile of liver-specific PTEN KO, PTEN/SCAP double KO mice

Project description:Nonalcoholic steatohepatitis (NASH), a severe form of nonalcoholic fatty liver disease, is characterized by hepatic steatosis and hepatocellular injury and progresss cirrhosis and hepatocellular carcinoma. Sterol regulatory elment-binding proteins (SREBPs) are master regulators of lipogenesis. Liver-specific PTEN knockout (KO) mice show constitutive upregulation of SREBP through PI3K-Akt pathway activation, leading to spontaneous fatty liver and subsequent HCC development. SREBP cleavage-activating protein (SCAP) plays a critical role in SREBP activation. We sought to determine the impact of SREBP inhibition on NASH and HCC development. To this end, we additionaly inhibited SREBP pathway in liver-specific PTEN mice by ablating SCAP and generated liver-specific PTEN/SCAP double KO (DKO) mice. However unexpectedly, inhibition of SCAP/SREBP pathway markedly exacerbated liver injury (5weeks), fibrosis (5months), and carcinogenesis (7 months) in PTEN KO mice. To elucidate the mechanisms of liver tumorigenesis in liver-specific PTEN/SCAP DKO mice, we conducted transcriptome analyses of the livers.

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MicroRNA profiling in Pten knockout mouse thymus cells

Project description:MicroRNA profiling in Pten knockout mouse thymus cells. microRNAs (miRs) are short noncoding RNAs of 20â22 nucleotides that function to regulate gene expression at the posttranscriptional level. They play fundamental roles in the regulation of cellular proliferation, differentiation, and apoptosis. miRs are dysregulated in many types of cancer, including T-ALL (T cell lymphoblastic leukemia). miRs can function as oncogenes, favoring the initiation and progression of cancers, or as tumor suppressors, preventing tumorigenesis. The biological functions of miRs in T-ALL are largely unknown. In human T-ALL patients, recurrent mutations in the Phosphatase and tensin homolog (PTEN) gene are common, consistent with Pten-knockout mice developing T-ALL. To better understand T-ALL pathogenesis and identify new therapeutic targets in T-ALL, we developed a Pten-knockout T-ALL mouse model and the mice developed T-ALL within 3 months as expected. We profiled the miRs in the Pten-deficient mouse T-ALL. A576, A577, A578 and A579 are PTEN-knockout mouse T-ALL samples. A580 andA 581 are wild-type mouse thymocytes.

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