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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

SUBMITTER: Lasse Sinkkonen

PROVIDER: E-GEOD-7141 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells.

Sinkkonen Lasse L Hugenschmidt Tabea T Berninger Philipp P Gaidatzis Dimos D Mohn Fabio F Artus-Revel Caroline G CG Zavolan Mihaela M Svoboda Petr P Filipowicz Witold W

Nature structural & molecular biology 20080302 3

Loss of microRNA (miRNA) pathway components negatively affects differentiation of embryonic stem (ES) cells, but the underlying molecular mechanisms remain poorly defined. Here we characterize changes in mouse ES cells lacking Dicer (Dicer1). Transcriptome analysis of Dicer-/- cells indicates that the ES-specific miR-290 cluster has an important regulatory function in undifferentiated ES cells. Consistently, many of the defects in Dicer-deficient cells can be reversed by transfection with miR-29 ...[more]

PMID: 18311153

Similar Datasets

siRNA of mouse undifferentiated Dicer -/- (27H10) embryonic stem cells

Project description:We have analyzed the transcript expression levels in Dicer knock-out embryonic stem (ES) cells 24 hours after transfection with either control siRNA agains Renilla luciferase or miRNA Mimics (Dharmacon) of mmu-miR-290 cluster members in order to identify primary targets of miR-290 cluster miRNAs. Experiment Overall Design: Cell were analysed 24h after transfections in an undifferentiated state. Triplicates of both transfections were analyzed.

2008-06-16 | E-GEOD-8503 | biostudies-arrayexpress

mRNA expression analysis of 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. Keywords: Cell type comparison of cell line with or without knock-out

2008-01-01 | GSE7141 | GEO

mRNA expression analysis of undifferentiated Dicer -/- (27H10) embryonic stem cells after miRNA transfection

Project description:We have analyzed the transcript expression levels in Dicer knock-out embryonic stem (ES) cells 24 hours after transfection with either control siRNA agains Renilla luciferase or miRNA Mimics (Dharmacon) of mmu-miR-290 cluster members in order to identify primary targets of miR-290 cluster miRNAs. Keywords: Comparison of effect of two different transfections on transcriptome of Dicer-KO ES cells

2008-01-01 | GSE8503 | GEO

Transcription profiling of human HEK-293 cells to identify Dicer and Argonaute regulated gene expression

Project description:HEK-293-derived cell lines depleted of Dicer or one of four Argonaute proteins were generated. Microarray analysis of these knock down cell lines and various control cell lines was performed to address how large the proportion of genes is that are regulated by RNA silencing in an individual cell type. Comparison of different arrays revealed commonly (up) regulated genes. The highest overlap was observed in Ago2 and Dicer knockdown cells. Experiment Overall Design: three control cell lines (T-Rex, shRNA, empty vector), two induvidual Argonaute 1 and 4 (Ago1kd, Ago4kd) knock down cell lines, one Argonaute 2 and 3 (Ago2kd, Ago3kd) and two induvidual Dicer knock down cell lines were analyzed as biological replicates

2008-06-12 | E-GEOD-4246 | biostudies-arrayexpress

Transcription profiling of mouse Abl pre-B cell lines with conditional deletion of dicer

Project description:Abelson virus (v-Abl)-transformed pre-B cell lines from BM of dcrfl/fl; R26R-yfp (4470; 4475) and dcrfl/+; R26R-yfp mice (4483) are treated with a transducible Cre protein (Tat-Cre) to induce deletion of the dicer-1 gene in vitro. Cre activity is conveniently monitored by concomitant expression of YFP. To obtain Dicer KO cells, YFP+ cells from dcrfl/fl; R26R-yfp (4470_YFP; 4475_YFP) cultures treated with Tat-cre were isolated by fluorescence-activated cell sorting (FACS) and further propagated in cell culture. As controls, we used non-deleted, YFP- cells sorted from dcrfl/fl; R26R-yfp cultures (4470; 4475) treated with Tat-cre, and YFP+ deleted cells from dcrfl/+; R26R-yfp cultures (4483_YFP). To validate this system, various cell populations were sorted and analyzed for Dicer protein and miRNA expression. In the Dicer KO pro-B cell lines, Western analysis indicated that Dicer protein was efficiently ablated, and Northern blots demonstrated that the levels of mature miR-17 and miR-191 were drastically reduced.

2008-03-08 | E-MEXP-1455 | biostudies-arrayexpress

Short RNA profiling of ES cells with and without Dicer

Project description:To better understand Dicer function, and the potential mechanisms by which RNAi contributes to pluripotency, short RNA expression was profiled from 4 ES cell libraries: 2 made from a Dicer-conditional ES cell line before and several months after deletion of Dicer, and 2 made before and 5 days after demethylation of J1 ES cells with 5-aza-deoxycytidine. Contributed here are the unannotated sequence data from each library, including those sequences that did not match the mouse genome or any known non-coding RNAs. Keywords: 454 sequencing, miRNA, dicer, demethylation

2007-10-31 | GSE9306 | GEO

Expression data from wild-type, Dgcr8 knockout and Dicer knockout ES cells

Project description:Dgcr8 and Dicer are both important components of the microRNA biogenesis pathway while Dicer is also implicated in biogenesis of other types of small RNAs such as siRNAs and mirtrons. Here we performed microarray analysis of WT, Dgcr8 and Dicer knockout ES cells to identify mRNAs differentially regulated upon loss of Dgcr8 and Dicer.

2009-09-23 | GSE16923 | GEO

Transcription profiling of mouse D4 and C2 ES cell lines assessed for chimerism and germline transmission

Project description:Two independent ES cell lines (D4 and C2) were assessed for chimerism and germline transmission. Although these lines were able to produce chimerism at early passage, no germ line transmission was seen. After passaging in a proprietary medium and subcloning by detaching loosely connected cells and culturing in the recommended medium, both lines experienced an increase in potential as evidenced by an enhanced ability to go germ line. Analysis of early passage, and late passage detached and attached cells will allow the determination of genes that may be implicated in the increase of potential seen in these cells. Note: additional replicates may be added at a later date. Experiment Overall Design: this experiment include 6 samples and 34 replicates

2008-06-12 | E-GEOD-4087 | 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 parthenogenetic embryonic stem cells and normal embryos to investigate imprinting

Project description:To identify the imprinting loci, we designed microarray analysis on the parthenogenetic embryonic stem cells and normal embryos. We could predict 217 imprinting domains associated with embryo development and maternal imprinting. Experiment Overall Design: Five embryonic stem (ES) cell lines were derived from two F1 hybrid strains that were produced by mating female C57BL6 mice with male DBA2 or CBA/Ca mice. Two-week-old prepubertal female was used for follicle retrieval. All procedures for animal management, breeding, and surgery followed the standard protocols of Seoul National University, Korea. The Institutional Animal Care and Use Committee Review Board at Seoul National University approved our research proposal in April 2005 (approval number: SNU0050331-02). Three parthonogenetic ES embryo cell lines were established from parthenogenetic activation on naturally ovulated oocytes (OpB6D2-SNU-1) and in vitro-growth oocytes (FpB6CBA-SNU8 and FpB6D2-SNU2). Two normal ES embryo cell lines were derived from mating naturally ovulated female mice in estrus with male mice (NmB6D2-SNU-1) and purchased from ATCC. Detailed procedures, including establishment of ES cell lines can be found elsewhere (FpB6CBA-SNU8, FpB6D2-SNU2 and OpB6D2-SNU-1 for and NmB6D2-SNU-1 and OP1 for manuscript in preparation).

2009-01-14 | E-GEOD-10776 | biostudies-arrayexpress

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