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ICLIP analysis of RNA binding sites of Stau2 protein in mouse brain cells

ABSTRACT: iCLIP analysis of RNA binding sites of Stau2 protein in mouse brain cells

PROVIDER: PRJEB20555 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1948353.fastq.gz	Fastqsanger.gz
	ERR1948354.fastq.gz	Fastqsanger.gz
	ERR1948355.fastq.gz	Fastqsanger.gz
	ERR1948356.fastq.gz	Fastqsanger.gz
	ERR1948357.fastq.gz	Fastqsanger.gz

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iCLIP analysis of RNA binding sites of Stau2 protein in mouse brain cells

Project description:Stau2 iCLIP of mouse brain was performed to identify RNA binding sites of Stau2 protein in mouse brain cells. The experiment was performed in triplicate, and each of the replicates was split into two separate halves at the cDNA stage, which together led to 6 separate datasets. The iCLIP protocol includes the following steps; Embryonic day 18 whole mouse brain was dissociated and irradiated with UV-C light, and the cells were then lysed using a buffer containing detergents. The RNAs were partially digested, and Stau2 and the cross-linked RNA fragments were immunoprecipitated using anti-Stau2 antibody. A DNA adaptor was then ligated to the RNA fragments and the cross-linked RNAs were further purified by SDS-PAGE and nitrocellulose membrane transfer. The RNAs were extracted from the membrane by proteinase K treatment, and converted into a high-throughput DNA sequencing compatible library by reverse transcription and PCR. For further details, see the methods of the associated manuscript. Note that the sequence reads start with (3 nucleotides of unique molecular identifiers) + (4 nucleotides of experimental barcode) + (2 nucleotides of unique molecular identifiers) followed by the sequence of the cross-linked RNA fragments.

2017-08-02 | E-MTAB-5703 | biostudies-arrayexpress

Rattus novegicus cerebral cortex hiCLIP mapping of STAU2 binding sites

Project description:Using an improved hiCLIP protocol (Lee & Chakrabarti et al.), we mapped the binding sites of STAU2 in rat cortex and their secondary structure context.

2021-12-04 | E-MTAB-11201 | biostudies-arrayexpress

Rattus novegicus cerebral cortex hiCLIP mapping of STAU2 binding sites

Project description:Rattus novegicus cerebral cortex hiCLIP mapping of STAU2 binding sites

| PRJEB49025 | ENA

iCLIP transcriptome-wide mapping of UNR (CSDE1) binding sites

Project description:iCLIP transcriptome-wide mapping of UNR (CSDE1) binding sites

| PRJEB10303 | ENA

Transcriptome-wide mapping of RNA binding sites of the RNA-binding protein Unkempt using iCLIP-seq

Project description:iCLIP experiments tomap the RNA binding sites of the RNA-binding protein Unkempt across the transcriptome in SH-SY5Y cells, HeLa cells with ectopic Unk expression and mouse E15 embryonic brain samples. Expression of Unk is normally largely restricted to the nervous system. We therefore mapped the binding sites in human SH-SY5Y and mouse E15 brain to detect its physiological binding sites (in SH-SY5Y, we also performed the RNAseq experiment upon Unk knockdown). HeLa cells on the other hand normally don't express Unk, but convert to neuron-like shape when the protein is ectopically expressed. So, here we hoped to identify those binding events (and hence target transcripts) that are critical for this morphological transformation.

2015-03-09 | E-MTAB-2279 | biostudies-arrayexpress

iCLIP seq reveals distribution of genome-wide SR protein-RNA binding

Project description:We identified the precise genome-wide binding sites for all SR proteins, using iCLIP-seq

2014-11-23 | GSE63262 | GEO

High-resolution analysis of SRSF3 and SRSF4 binding sites by iCLIP

Project description:Endogenous SRSF3 and SRSF4 RNA binding sites were identified genome-wide by iCLIP in P19 BAC trangenic cell lines using GFP-epitope tag.

2012-03-21 | E-MTAB-747 | biostudies-arrayexpress

Transcriptome-wide mapping of RNA binding sites of the RNA-binding protein Unkempt using iCLIP-seq

Project description:Transcriptome-wide mapping of RNA binding sites of the RNA-binding protein Unkempt using iCLIP-seq

| PRJEB5286 | ENA

High-resolution analysis of SRSF3 and SRSF4 binding sites by iCLIP

Project description:High-resolution analysis of SRSF3 and SRSF4 binding sites by iCLIP

| PRJEB2638 | ENA

Sequencing of RNA Isolated Through RNA Immunoprecipitation (RIP) of Murine Cortical Tissue Using STAU2 Antibody

Project description:We report here the sequencing and analysis of RNA isolated through RNA immunoprecipitation (RIP) of embryonic mouse cortical tissue. STAU2 antibodies were used to perform these RIPs at four different ages, and the RNA was compared against matching input samples. This allowed characterization of putative STAU2 binding sites in different RNA classes over the course of development, important as STAU2 is a known double-stranded RNA binding protein with a role in asymmetric division of neural progenitor cells.

2021-01-30 | GSE110484 | GEO

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