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Mus musculus

ABSTRACT: Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

PROVIDER: PRJNA134881 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR072951.fastq.gz	Fastqsanger.gz
	SRR072952.fastq.gz	Fastqsanger.gz
	SRR072953.fastq.gz	Fastqsanger.gz
	SRR072954.fastq.gz	Fastqsanger.gz
	SRR072955.fastq.gz	Fastqsanger.gz

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Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

2011-01-10 | GSE25310 | GEO

Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

Project description:MicroRNAs (miRNAs) are a large family of 19-22nt non-coding RNAs that post-transcriptionally regulate their mRNA targets. Computational algorithms predict that over half of all genes are regulated by miRNAs, yet approaches for experimental identification of miRNA binding sites are now emerging. To directly identify endogenous miRNA binding sites, we performed photo-crosslinking immunoprecipitation using antibodies against Ago2, followed by deep-sequencing of RNA tags (CLIP-seq) in mouse embryonic stem cells (mESCs). We also performed parallel CLIP-seq in Dicer null mESCs that lack mature miRNAs, allowing us to define whether the association of Ago2 with the identified sites was mediated by miRNAs. We include the exon-array expression data obtained from three sets of Dicer WT and Dicer Null mESCs.These data are used to determine genes that are differentially expressed between Dicer WT and Dicer Null conditions. Six samples (3 Dicer wild-type CLIP RNA libraries representing two biological replicates, 2 Dicer null CLIP RNA libraries, 1 short-RNA library from Dicer wild-type mESCs) were analyzed. Six total mESC samples were analyzed (3 Dicer WT, 3 Dicer Null). Expression values for probesets were summarized into a single per-gene value. The log fold change for Dicer_WT/Dicer_Null was defined as the difference between the mean expression in Dicer WT mESCs and the mean expression in the Dicer Null mESCs.

2011-01-10 | E-GEOD-25310 | biostudies-arrayexpress

Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [4_Cnot shRNA-seq]

Project description:Here, we show that embryonic stem cells (ESCs) and muscle stem cells contain high levels of nuclear AGO proteins and that in ESCs nuclear AGO2 protein activity is sufficient to allow for differentiation. Transcriptome-wide mapping of binding sites at nucleotide resolution revealed that nuclear AGO2 expands its target sequence repertoire in a miRNA-dependent manner to include intronic sequences to induce post-transcriptional gene silencing

2018-08-31 | GSE108798 | GEO

Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [3_RNA-seq]

2018-08-31 | GSE108797 | GEO

Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [2_PAR-CLIP]

2018-08-31 | GSE108795 | GEO

Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [1_Differentiation_rna_seq]

2018-08-31 | GSE108794 | GEO

Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [6_chr_seq]

2018-08-31 | GSE108800 | GEO

Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [5_miRNA-seq]

2018-08-31 | GSE108799 | GEO

Convergence of distinct RNA-silencing pathways on GW182/Tnrc6

Project description:The RNA-binding protein Trim71/Lin41 is a phylogenetically conserved developmental regulator that functions in mammalian stem cell reprogramming, brain development and cancer. Trim71 recognizes target mRNAs through hairpin motifs and silences them through molecular mechanisms that await identification. Deposited data are mass spectrometry data from immunoprecipitation experiments with endogenously tagged Trim71, Ago2, and Tnrc6a. Experiments are carried out in mouse embryonic stem cells (mESCs) and uncover reciprocal interactions of Trim71, Ago2, and Tnrc6a. Trim71 protein interactions are largely independent of Ago2 levels, but strongly depend on the presence of RNA. A second set of experiments is mass spectrometry data from immunoprecipitation experiments in mESCs overexpressing a tagged peptide derived from Homo sapiens TNRC6B (‘FLAG-HA::T6BWT::Cherry’), that is known to block the Tnrc6-Ago2 interaction. We show that a wild-type version strongly binds Ago1 and Ago2, but not Trim71, while a mutant version binds neither Ago1, 2, nor Trim71.

2023-07-04 | PXD034537 | Pride

LIS1 RNA binding orchestartes the mechanosensitive properties of embryonic stem cells in AGO2 dependent and independent ways.

Project description:LIS1 immunoprecipitation in nuclear and cytoplasmic fractions of LIS1 Floxed/-, OE and WT embryonic stem cells. To identify AGO2 dependent and independent interactions LIS1 was immunoprecipitated in AGO1-4 knockout and doxycycline induced AGO2 mouse embryonic stem cells.

2023-07-20 | PXD033150 | Pride

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