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Expression data from Dicer WT and Dicer KO mouse CD4 T cells.

ABSTRACT: miRNA regulate gene expression at the post-transcriptionnal level. To gain further insight into this process, we analysed by Affymetrix microarray, the transcriptome of Dicer WT or Dicer deleted mouse CD4 T cells. Mouse CD4 T cells were sorted by flow cytometry from control CD4Cre neg Dicer lox/lox or CD4Cre pos Dicer lox/lox animals, total RNA was extracted using RNA bee and amplified before hybridization onto Mouse Gene arrays. Three biological replicate were analysed for each condition (3 Dicer WT control and 3 Dicer KO).

ORGANISM(S): Mus musculus

SUBMITTER: Gopuraja Dharmalingam

PROVIDER: E-GEOD-59848 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from Dicer WT and Dicer KO mouse CD4 T cells.

Project description:miRNA regulate gene expression at the post-transcriptionnal level. To gain further insight into this process, we analysed by Affymetrix microarray, the transcriptome of Dicer WT or Dicer deleted mouse CD4 T cells.

2015-02-15 | GSE59848 | GEO

Gene expression profile of Dicer knockout in mouse DP thymocytes

Project description:The RNase III enzyme dicer is essential for the processing of microRNAs (miRNAs) and small interfering RNAs (siRNAs) from double-stranded RNA precursors. miRNAs and siRNAs regulate chromatin structure, gene transcription, mRNA stability and translation in a wide range of organisms. To provide a model system to explore the role of dicer-generated RNAs in the differentiation of mammalian cells in vivo, we have generated a conditional dicer allele. Deletion of dicer at an early stage of T cell development compromised the survival of αβ lineage cells, while the numbers of γδ-expressing thymocytes were not affected. In developing thymocytes, dicer was not required for the maintenance of transcriptional silencing at pericentromeric satellite sequences (constitutive heterochromatin), the maintenance of cytosine DNA methylation and X chromosome inactivation in female cells (facultative heterochromatin) and the stable shutdown of a developmentally regulated gene (developmentally regulated gene silencing). Most remarkably, given that one-third of mammalian mRNAs are putative miRNA targets, dicer appears to be dispensable for CD4/8 lineage commitment, a process where epigenetic regulation of lineage choice has been well documented. Thus, although dicer appears critical for the development of the early embryo, it may have limited impact on the implementation of lineage-specific gene expression programs. LckCre was used to delete a floxed Dicer1 allele from developing thymocytes (Cobb BS, Nesterova TB, Thompson E, Hertweck A, O'Connor E, Godwin J, Wilson CB, Brockdorff N, Fisher AG, Smale ST and Merkenschlager M. T cell lineage choice and differentiation in the absence of the RNAse III enzyme dicer. J. Exp. Med. 2005 201: 1367-1373). Thymocytes were stained for CD4 and CD8, and double-positive (DP) thymocytes were sorted by flow cytometry. Three biological replicates of Dicer lox/lox control samples and LckCre Dicer lox/lox KO samples were analysed.

2015-01-28 | E-GEOD-57511 | biostudies-arrayexpress

DICER-interacting partners in juvenile mouse testes

Project description:DICER has a well-characterized role in the processing of microRNAs (miRNAs) and small interfering RNAs (siRNA) that are important for post-transcriptional gene regulation. Emerging evidence suggests that DICER also has several non-canonical functions beyond miRNA/siRNA biogenesis, for example in transcriptional gene silencing at the chromatin level, as well as in RNA degradation and maintenance of genomic integrity. We have shown that the function of DICER in germ cells is essential for normal spermatogenesis; male mice lacking DICER in postnatal male germ cells are infertile due to severe defects in haploid differentiation. To better understand the function of DICER in male germ cells, we immunoprecipitated DICER from juvenile mouse testes and performed mass spectrometric analysis to identify DICER-interacting proteins.

2020-06-03 | PXD017772 | Pride

Transcription profiling of mouse undifferentiated Dicer +/- (D4) and Dicer -/- (27H10) embryonic cell lines

Project description:We have analyzed the transcript expression levels in Dicer heterozygous and Dicer knock-out embryonic stem (ES) cells in order to identify which transcripts are regulated by RNAi pathway in mouse ES cells. Experiment Overall Design: Two cell lines were analysed in an undifferentiated state. Triplicates of both cell lines were analyzed.

2008-06-15 | E-GEOD-7141 | biostudies-arrayexpress

DICER controls macrophage polarization and tumor response to immunotherapy

Project description:Tumor-associated macrophages (TAMs) have immunosuppressive capacity in mouse models of cancer. Here we show that the genetic deletion of the microRNA (miRNA)-processing enzyme DICER in TAMs broadly programs them to a CD11c+MRC1â/low M1-like immunostimulatory phenotype characterized by activated interferon-Î³ (IFN-Î³)/STAT1/IRF signaling. M1-like TAM programming fostered the recruitment of cytotoxic T-cells (CTLs), including tumor-antigen-specific CTLs, inhibited tumor growth, and enhanced the efficacy of PD1 checkpoint blockade. Bioinformatics analysis of TAM transcriptomes identified a limited set of miRNAs putatively involved in TAM programming. Re-expression of Let-7 in Dicer-deficient TAMs was sufficient to partly rescue the M2-like (protumoral) TAM phenotype and abate tumor CTL infiltration. Targeted suppression of DICER activity in TAMs may, therefore, stimulate antitumor immunity and enhance the efficacy of cancer immunotherapy. To explore the role of DICER in the development, activation and immunological functions of TAMs, we crossed homozygous LysM-Cre (Clausen et al., 1999) with Dicerlox/lox (Harfe et al., 2005) mice to obtain mice with myeloid-cell-specific Dicer1 gene deletion (LysM-Cre;Dicerâ/â, referred to as Dâ/â). These mice were then backcrossed to LysM-Cre to obtain the control LysM-Cre; Dicer+/+ mice (referred to as D+/+). Both LysM-Cre and Dicerlox/lox mutations were always homozygous in our experiment. We then inoculated Lewis lung carcinoma (LLC) cells subcutaneously (s.c.) in Dâ/â and control D+/+ mice. Once the tumors were established, we isolated by fluorescence-activated cell sorting (FACS) tumor-associated macrophages (F4/80+ cells).

2016-06-13 | E-GEOD-76356 | biostudies-arrayexpress

Gene expression changes in CD4+ thymocytes upon removal of Cullin3

Project description:We report gene expression changes in Cul3 deficient thymic CD4+ T cells We used microarrays to detail the global programme of gene expression changes upon removal of Cul3 during thymic development CD25-, CD1dPBS57-, gdTCR - CD4+ Single positive cells from thymocytes of CD4Cre-Cul3fl/fl (LM) and CD4 Cre+Cul3fl/fl (KO) were sort purified and total RNA was extracted using Trizol and analysed by microarray.

2014-04-05 | E-GEOD-56514 | biostudies-arrayexpress

Phosphoproteomic analysis of liver of Dicer knockout mice

Project description:Dicer is an essential ribonuclease involved in the biogenesis of miRNA. Previous studies have reported that Dicer is dysregulated in multiple types of cancers. To investigate the downstream phosphoproteome of Dicer, we carried out phosphotyrosine profiling of the liver of Dicer knockout of mice. We employed antibody-based enrichment of phosphotyrosine containing peptides coupled with spike-in SILAC-based quantitation. Over 400 phosphoisites were identified in each condition while 290 phosphosites were quantitated in common. Amongst these, several key signaling molecules like receptor tyrosine kinase MET, MET, PDGFR, EPHA2, EPHB4 and IGF1R/INSR were hyperphosphorylated. Also, non-receptor tyrosine kinases of Src family and their downstream effector signaling partners including IRS2 and STAT3were found to be hyperphosphorylated. Our study indicates that there is significant alteration in the signaling pathways upon ablation of Dicer.

2016-07-08 | PXD000927 | Pride

Effect of Embigin on LTA1 induced-CD4+ TRM cells.

Project description:To investigate the function of Embigin on LTA1 induced-CD4+TRM cells, we immunized CD4cre x Embfl/fl mice with OmpX and LTA1 at Day0 and Day21, and isolated CD4+ cells from Embfl/fl CD4cre-(WT) and Embfl/fl CD4cre+(KO) mice from the lung by magnetic beads. We then performed gene expression profiling analysis using data obtained from RNA-seq of CD4+cells from 5 WT and 5 KO mice.

2024-01-21 | GSE253411 | GEO

RNA sequencing of naïve, Th1 and Th2 polarised live CD4+ T cells from CD4Cre+ and CD4Cre+DOT1LFL/FL mice

Project description:RNA sequencing of naïve, Th1 and Th2 polarised live CD4+ T cells from CD4Cre+ and CD4Cre+DOT1LFL/FL mice

2020-12-15 | GSE123966 | GEO

Murine platelet miRNA pattern and its regulation by a MK/platelet-specific genetic ablation of Dicer.

Project description:Purpose: To assess the platelet miRNA pattern which is regulated in a Dicer-dependent manner, we conducted a global screen of platelet miRNA expression of murine platelets from Dicerlox/lox and DicerPf4∆/Pf4∆ mice using Next-generation deep sequencing analysis. Methods: Platelets were isolated from 10- to 12-week-old Dicerlox/lox and DicerPf4Δ/Pf4Δ mice of male sex. Total RNA including miRNA was isolated from murine platelets using the QIAsymphony RNA Kit. The sequencing library was prepared using the QIAseq miRNA Library Kit with 10 to 20 ng input. The libraries were pooled in an equimolar fashion and sequenced on a NovaSeq6000 as paired-end reads with a sequencing depth of >12 Mio clusters (i.e. read-pairs) per sample. Results: we were able to detect a total of 427 miRNAs in these platelets, of which 81 were significantly regulated (> |0.5| logFC threshold) in a Dicer-dependent manner. The majority of miRNAs were significantly downregulated, but a smaller proportion of miRNAs was slightly, but significantly upregulated in platelets lacking Dicer. Conclusions: this study discloses differential expression patterns of further platelet miRNAs that potentially link multiple intercellular processes and pathways implicated in several stages of the pathogenesis of myocardial I/R injury

2023-03-03 | GSE184523 | GEO

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