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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE221020 | GEO | 2023/09/01

REPOSITORIES: GEO

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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

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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.

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

2014-11-14 | GSE63273 | GEO

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