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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

Engineering spacer specificity of the Cre/loxP system

Project description:Translational research on the Cre/loxP recombination system focuses on enhancing its specificity by modifying Cre/DNA interactions. Despite extensive efforts, the exact mechanisms governing how Cre distinguishes between substrates remains elusive. Cre recognizes 13 bp inverted repeats, initiating recombination in the 8 bp spacer region. While literature suggests that efficient recombination proceeds between lox sites with non-loxP spacer sequences when both lox sites have matching spacers, experimental validation for this assumption is lacking. To fill this gap, we investigated target site variations of identical pairs of the loxP 8 bp spacer region, screening 6,000 unique loxP-like sequences. Approximately 84% of these sites exhibited efficient recombination, affirming the flexibility of spacer sequences for catalysis. However, certain spacers negatively impacted recombination, emphasizing sequence dependence. Directed evolution of Cre on inefficiently recombined spacers not only yielded recombinases with enhanced activity but also mutants with reprogrammed selective activity. Mutations altering spacer specificity were identified, and molecular modelling and dynamics simulations elucidated the mechanism behind this specificity switch. These findings highlight the potential to fine-tune site-specific recombinases for spacer sequence specificity, offering a novel concept to enhance the applied properties of designer-recombinases for genome engineering applications.

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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

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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.

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

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

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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).

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