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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression in IRfl/fl Cre- and IRfl/fl Cre+ mice

ABSTRACT: The floxed insulin receptor was specifically targetted for deletion in the mammary gland using a mouse strain bearing Cre recombinase under the BLG promoter. Data analysis: Genespring was used for data analysis All entities (28853) were filtered on variance between samples, eliminating from further analysis of genes whose coefficient of variation was greater than 50%. The remaining 2239 genes were filtered on expression levels between 20 and 20,000 intensity units An unpaired T-test was used to find genes that differed significantly (P<0.05) between experimentals and controls The remaining 2014 genes were filtered for a 1.1 absolute fold change between experimentals and controls. Of the remaining expression of 890 genes was down in the Cre+ mice and expression was up for 457 genes in the Cre+ mice. Mouse strains containing a floxed insulin receptor (IRfl/fl) were crossed with a mouse expressing Cre recombinase from a BLG promoter RNA was applied to Affymetrix MoGene_1_0-st-v1 chips Three replicates from each strain were used for analysis.

ORGANISM(S): Mus musculus

SUBMITTER: Margaret Neville

PROVIDER: E-GEOD-48009 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression in IRfl/fl Cre- and IRfl/fl Cre+ mice

Project description:The floxed insulin receptor was specifically targetted for deletion in the mammary gland using a mouse strain bearing Cre recombinase under the BLG promoter. Data analysis: Genespring was used for data analysis All entities (28853) were filtered on variance between samples, eliminating from further analysis of genes whose coefficient of variation was greater than 50%. The remaining 2239 genes were filtered on expression levels between 20 and 20,000 intensity units An unpaired T-test was used to find genes that differed significantly (P<0.05) between experimentals and controls The remaining 2014 genes were filtered for a 1.1 absolute fold change between experimentals and controls. Of the remaining expression of 890 genes was down in the Cre+ mice and expression was up for 457 genes in the Cre+ mice.

2013-06-18 | GSE48009 | GEO

Mouse retina from Msi1/Msi2 double knockout in photoreceptor cells

Project description:This quantitative protepomics study (TMT10 isobaric labeling) of the protein expression in the retina of Msi1/Msi2 double knockout mouse compared to floxed controls. The Msi1 and Msi2 genes were knocked out in photoreceptor cells using tamoxifen inducible Cre (Cre-ERT2) under the control of Pde6g promoter. Tamoxifen was administered by intrapertoneal injection for three consecutive day starting at postnatald day 30, and the retina was collected at postnatal day 51. Retinas from floxed animals lacking the Cre recombinase and treated with tamoxifen were used as controls. Five biological replicates for each knockout (three femailes, two males) and control (two femaes and three males) group were used.

2022-03-10 | PXD030748 | Pride

Effect of the combined loss of tomosyn (STXBP5) and tomosyn-2 (STXBP5L) on the proteome of primary mouse hippocampal neurons

Project description:Tomosyn (STXBP5) is a non-canonical SNARE protein enriched in many secretory cells and implicated in regulation of exocytosis. In neurons, loss of tomosyn affects fusion of synaptic vesicles. Here, we examined the impact of the loss of tomosyn (STXBP5) and its close paralog, tomosyn-2 (STXBP5L), on the proteome of primary mouse hippocampal neurons. To do this, we used a mouse model carrying floxed alleles of Stxbp5 and Stxbp5l genes. Primary hippocampal neurons isolated from these mice were transduced with Cre-recombinase, which expression resulted in a nearly complete loss of the two genes expression. As control, we used neurons from the same culture preparation but expressing Cre-recombinase lacking DNA-binding domain (ΔCre). This dataset provides the comparison of proteome of control ('WT') and Stxbp5/5l double knockout ('DKO') neurons.

2022-12-19 | PXD038442 | Pride

Expression data from mouse livers expressing or lacking Cre recombinase during pneumonia

Project description:Cre-recombinase expression under control of an albumin promoter in the presence of floxed alleles is a highly effective and specific way to target gene mutations in hepatocytes. However, some concerns have been raised regarding off-target and/or toxic effects of cre itself, possibly confounding the interpretation of studies employing this approach. We have now used this tool to succesfully target gene deletions in hepatocytes during pneumonia, a condition which results in significant remodeling of the hepatic transcriptome. The goal of this study was to determine what effects, if any, cre expression alone has on hepatic gene expression during bacterial pneumonia. Mutant mice expressed CRE-recombinase under control of an albumin promoter. Results from mutants were compared to wild-type mice on the same genetic background (C57BL/6). Microarray analysis was performed on liver RNA collected from both genotypes of mice in the absence and presence of pneumococcal pneumonia.

2012-02-16 | GSE35515 | GEO

A novel Cpa3-Cre; miR-9∆fl/∆fl mouse reveals a functional role for miR-9 in promoting a mast cell invasive phenotype via upregulation of CMA1

Project description:The purpose of this study was to investigate the biologic consequences of miR-9 overexpression in normal mast cells and interrogate the mechanisms by which mir-9 enhances invasion. We generated a transgenic mouse line carrying a floxed-STOP-miR-9 transgene (miR-9∆fl/∆fl) and crossed it with Cpa3-Cre transgenic mice in which Cre recombinase expression is restricted largely to mast cells and basophils, by the carboxypeptidase A3 (Cpa3) promoter. RNA-seq revealed a unique transcriptional profile associated with miR-9 overexpression in BMCMCs, notably up-regulation of mast cell-restricted proteases CMA1 and MCP6 involved in extracellular matrix remodeling. Targeting of the transcriptional corepressor SIN3A by miR-9 enhanced CMA1 expression, indicating a novel regulatory pathway through which miR-9 upregulates CMA1 expression, thereby promoting an invasive phenotype. These data support a role for miR-9 in mast cell invasive properties and provide a mechanism through which dysregulation of miR-9 in mast cells may contribute to pathologic conditions involving mast cell-mediated tissue remodeling.

2018-10-11 | GSE121076 | GEO

Characterization of mu opioid receptor cells in a new Oprm1-cre mouse

Project description:we derived, validated, and applied a novel MOR-specific Cre mouse line, inserting a T2A cleavable peptide sequence and the Cre coding sequence into the MOR 3’UTR. Importantly, this line shows specificity and fidelity of MOR expression throughout the brain and with respect to function, there were no differences in behavioral responses to morphine when compared to wild type mice, nor are there any alterations in Oprm1 gene expression or receptor density. To assess Cre recombinase activity, MOR-Cre mice were crossed with the floxed GFP-reporters, RosaLSLSun1-sfGFP or RosaLSL-GFP-L10a. The latter allowed for cell type specific RNA sequencing via TRAP (Translating Ribosome Affinity Purification) of striatal MOR+ neurons following opioid withdrawal.

2023-01-01 | GSE218564 | GEO

Expression data from mouse livers expressing or lacking Cre recombinase during pneumonia

2012-02-16 | E-GEOD-35515 | biostudies-arrayexpress

Comparison of gene expression signatures between Cre- KTC organoid organoid and Cre+ KTC organoid

Project description:To identify downstream genes involved in cholangiocarcinoma development by genetic manipulations of Kras, TGFbR2, and CDH1, we cultured the biliary organoid from the extrahepatic bile duct of Cre-negative LSL-KrasG12D;Tgfbr2flox/flox;CDH1flox/flox (KTC) mice, and induced gene recombination using a lentivirus expressing Cre-recombinase (Cre+ KTC organoid) or control lentivirus (Cre- KTC organoid). Then, we compared gene expression signatures between Cre- KTC organoid organoid and Cre+ KTC organoid.

2017-04-30 | GSE88900 | GEO

Expression data of mouse calvarial stem cells from p75 floxed mice (p75fl/fl) stimulated with Adenovirus encoding Cre recombinase (Ad-Cre) or control (Ad-GFP) [RNA-seq]

Project description:Expression data of mouse calvarial stem cells from p75 floxed mice (p75fl/fl) stimulated with Adenovirus encoding Cre recombinase (Ad-Cre) or control (Ad-GFP) [RNA-seq]

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RNA sequencing of Mpc1 floxed mouse prostate organoids transduced with RFP control or Cre virus and treated -/+ small molecule MPC inhibitor UK5099

Project description:The goal of this study was to determine how knockout or pharmacological inhibition of the mitochondrial pyruvate carrier (MPC) alters lineage identity in the prostate. We isolated basal cells from Mpc1 floxed mouse prostates and transduced with a control RFP virus or Cre recombinase virus. We then plated into organoid culture and treated with either vehicle or the small molecule MPC inhibitor UK5099 for one week.

2023-09-01 | GSE221022 | GEO

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