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Study on the genomic changes in ColIa2 Cre x RBP-Jkappa loxp/loxp mice

ABSTRACT: Skin tumor formed in the ColIa2 Cre x RBP-Jkappa loxp/loxp mice was analyzed for genomic changes by comparing with normal tissues from the same mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE36464 | GEO | 2012/05/01

SECONDARY ACCESSION(S): PRJNA153561

REPOSITORIES: GEO

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Study on the genomic changes in ColIa2 Cre x RBP-Jkappa loxp/loxp mice

Project description:Skin tumor formed in the ColIa2 Cre x RBP-Jkappa loxp/loxp mice was analyzed for genomic changes by comparing with normal tissues from the same mice. Genomic DNA were isolated from each individual tumor and compared with the DNA extracted from the brain tissue in the same mouse.

2012-04-30 | E-GEOD-36464 | biostudies-arrayexpress

Cre-loxP-induced Ewsr1-Atf1 translocation tumors

Project description:Cre-loxP-induced Ewsr1-Atf1 translocation tumors

| PRJNA666346 | ENA

Transcription profiling of prostate tumors derived from the PSA-Cre;PtenLoxP/LoxP mouse prostate cancer model

Project description:1. Comparison of gene expression profiles of normal prostates, hyperplastic prostates (4-5 month old mice) and prostate tumors (>10 month old mice) isolated from PSA-Cre;Pten-loxP/loxP mice 2.Comparison of the gene expression profiles and molecular subtyping of prostate tumors isolated from targeted Pten knockout mice

2016-09-30 | E-MTAB-3970 | biostudies-arrayexpress

Differential gene expression analysis for BAL cells isolated from LysM Cre and Netrin1loxp/loxp LysM Cre mice after intratracheal LPS challenge

Project description:Purpose: The goal of this study is to compare NGS-derived transcriptome profiling (mRNA-seq) of expressed genes between LysM Cre and Netrin1loxp/loxp LysM Cre mice 3 days after intratracheal LPS challenge in order to explain the worsened outcomes and increased levels of inflammation we measure in the Netrin1loxp/loxp LysM Cre mice Methods: Three days after mice were treated with intratracheal injections of LPS, BAL cells were collected and then depleted for neutrophils using antibody-mediated depletion. The remaining cells were used for RNA isolation. mRNA profiles were generated by deep sequencing, in quadruplicate (one sample in the Netrin1loxp/loxp LysM Cre group was excluded as the sequence depth was only half compare to other 3 replicates), using paired-end 75-cycle sequencing on an Illumina NextSeq 550 System. Bases with quality scores < 20 and adapter sequences were removed from raw data with Cutadapt (v1.15), followed by alignment of clean RNA-seq reads to GRCm38 with STAR(v2.5.3a). Gene abundance was counted by HTseq-count uniquely-mapped reads number with default parameter using GencodeM15. Genes with > 5 reads in at least one sample were included for differential expression analysis by DESeq2 software.

2021-02-24 | GSE167333 | GEO

RNA-seq for blood Ly6Chi and Ly6Clo monocyte in WT and RBP-Jfl/fl Lyz2-Cre mice

Project description:To evaluate the consequences of RBP-J loss of function in blood monocyte subsets, we sequenced RNA of blood Ly6Chi monocyte and Ly6Clo monocyte from WT and RBP-Jfl/fl Lyz2-Cre mice.

2024-02-26 | GSE208772 | GEO

RNAseq from mouse Cre-loxP-induced Ewsr1-Atf1 translocation

Project description:RNAseq from mouse Cre-loxP-induced Ewsr1-Atf1 translocation

| PRJNA666360 | ENA

Genome-wide transcriptional regulation by RBP-J

Project description:We sequenced mRNAs from bone borrow derived macrophages derived from the control (WT) and RBP-J conditional knockout mice (RBP-J KO; Rbpj f/f;LysM cre).

2016-12-01 | GSE53218 | GEO

Genome-wide microRNA expression in WT and RBP-J KO BMDMs

Project description:RBP-J is a master transcriptional factor of Notch signaling, which plays important roles in developmental processes as well as regulating macrophage-mediated inflammatory responses. However, the regulation of RBP-J on miRNAs are less studied. So we sequenced microRNAs from BMDMs derived from the LyZ2 Cre control (WT) and RBP-J conditional knockout mice (RBP-J KO; Rbpjf/f LyZ2 Cre) to address the roles of RBP-J on regulating miRNAs in macrophages.

2019-12-11 | GSE103220 | GEO

Mus musculus

Project description:Study on the genomic changes in ColIa2 Cre x RBP-Jkappa loxp/loxp mice

| PRJNA153561 | ENA

Bulk RNA sequencing of endothelial-derived and non-endothelial-derived BMSCs and OLCs of VE-Cadherin-Cre;LoxP-tdTomato mice

Project description:We performed lineage tracing experiments using VE-Cadherin-Cre;LoxP-tdTomato mice. In these mice, endothelial cells (ECs) and their progeny are permanently marked by tdTomato fluorescence. We found that a substantial subset of stromal cells is derived from ECs, as indicated by their tdTomato expression. These findings support the notion that endothelial to mesenchymal transition (EndoMT) contributes to hematopoietic bone marrow niche formation in mice. Here we sought to determine the transcriptomic differences between endothelial-derived (tdTomato-positive) and non-endothelial-derived (tdTomato-negative) bone marrow stromal cells (BMSCs) and osteo/chondrolineage progenitor cells (OLCs). Murine niche populations were obtained from collagenased bone fraction of VE-Cadherin-Cre;LoxP-tdTomato mice at 3 weeks (n=2) or 11 weeks (n=2) of age. BMSCs (CD45-TER119-CD31-CD144-SCA-1+ CD51+ cells) and OLCs (CD45-TER119-CD31-CD144-Sca1-CD51+ cells) were FACS-purified and sequenced.

2021-01-25 | E-MTAB-10020 | biostudies-arrayexpress

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