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Mus musculus

ABSTRACT: Argonaute HITS-CLIP in wild-type and APOBEC1-deficient BMDMs

PROVIDER: PRJNA253525 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1460500.fastq.gz	Fastqsanger.gz
	SRR1460501.fastq.gz	Fastqsanger.gz
	SRR1460502.fastq.gz	Fastqsanger.gz
	SRR1460503.fastq.gz	Fastqsanger.gz
	SRR1460498.fastq.gz	Fastqsanger.gz

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Argonaute HITS-CLIP in wild-type and APOBEC1-deficient BMDMs

Project description:To investigate the possible consequences of APOBEC1 editing for miRNA targeting, high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) of the Argonaute (Ago) proteins (Chi et al., 2009) was performed in BMDMs derived from wild-type and Apobec1-/- littermates.

2017-11-21 | GSE58798 | GEO

Mus musculus

Project description:Ribosome profiling in wild-type and APOBEC1-deficient BMDMs

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Project description:NOVA2 and NOVA1 HITS-CLIP in wild-type mouse cortex (E18.5)

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Gene expression profiling in VRK1-deficient testis of Mus musculus

2011-12-30 | GSE22674 | GEO

Gene expression profiling in VRK1-deficient testis of Mus musculus

Project description:To study effect of VRK1 deletion on spermatogenesis of the mouse, transciptomic analysis of genes in postnatal 8-day testicular cells of wild type and VRK1-deficient Mus musculus was performed. Gene expression in testes from from wild type and VRK1-deficient mutant Mus musculus, respectively, was measured. Four independent experiments for wild type and mutant, respectively, were performed.

2011-12-30 | E-GEOD-22674 | biostudies-arrayexpress

Camk2a-neuron specific FLAG-Ago HITS-CLIP

Project description:The HITS-CLIP procedure was used to detect miRNA mediated Argonaute (Ago) binding in Camk2a mouse neurons.

2023-01-31 | GSE211552 | GEO

AGO CLIP reveals an activated network for acute regulation of brain glutamate homeostasis in ischemic stroke [dataset 6]

Project description:Human motor cortex (brodmann’s area 9) tissues analyzed by Argonaute HITS-CLIP to determine human transcriptome-wide AGO binding pattern.

2019-06-14 | GSE104048 | GEO

Mus musculus

Project description:Cell type-specific HITS-CLIP reveals differential RNA processing in motor neurons

| PRJNA290852 | ENA

Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts.

Project description:High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) allows for high resolution, genome-wide mapping of RNA-binding proteins. We found that substantial mispriming during reverse transcription results in the overrepresentation of sequences complementary to the primer used for reverse transcription. Up to 45% of peaks in publicly available HITS-CLIP libraries are attributable to this artifact, and the majority of libraries have detectable levels of mispriming. We also found that standard techniques for validating miRNA-target interactions fail to differentiate between artifactual peaks and physiologically relevant peaks. Here, we present a modification to the HITS-CLIP protocol that effectively eliminates this artifact. Argonaute HITS-CLIP on the MCF-7 breast cancer cell line treated with 17Î²-estradiol for 0, 6 or 24 hours using a nested reverse transcriptions pimer and protected or unprotected reverse PCR primers for library amplification.

2016-02-19 | E-GEOD-78059 | biostudies-arrayexpress

Ago HITS-CLIP in KSHV-infected primary effusion lymphoma (PEL) cell lines BCBL-1 and BC-3

Project description:We performed Ago HITS-CLIP to identify targets of viral and human miRNAs in latently KSHV-infected PEL cells Ago HITS-CLIP was performed in two latently infected PEL cell lines, BCBL-1 and BC-3; Argonaute-immunoprecipitation of UV cross-linked Ago-miRNA-mRNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina GAxII); we performed 3 biological replicates for each cell line, two technical (sequencing) replicates of BCBL-1 biological replicate 1

2012-10-05 | E-GEOD-41357 | biostudies-arrayexpress

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