Rattus novegicus cerebral cortex hiCLIP mapping of STAU2 binding sites
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB49025 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR7428840.fastq.gz | Fastqsanger.gz | |||
| ERR7428841.fastq.gz | Fastqsanger.gz | |||
| ERR7428842.fastq.gz | Fastqsanger.gz | |||
| ERR7428843.fastq.gz | Fastqsanger.gz | |||
| ERR7428844.fastq.gz | Fastqsanger.gz |
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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
Project description:The double-stranded RNA binding protein Staufen2 (Stau2) is asymmetrically localized and segregated during asymmetric cell divisions in the developing mouse cortex and promotes intermediate progenitor cell fate. We carry out RNA immunoprecipitation with a Stau2 specific antibody, followed by microarray analysis to identify Stau2 assoicated RNAs that may be shuttled asymmetrically into one daughter cell thus affecting cell fate. Cortex was dissected from E13-14 timed-pregnant Swiss Webster Mice (Taconic) and RNA immunoprecipitation followed by microarray analysis was carried out to identy Stau2 associated RNA cargos.
2012-12-21 | E-GEOD-38222 | biostudies-arrayexpress
Project description:The double-stranded RNA binding protein Staufen2 (Stau2) is asymmetrically localized and segregated during asymmetric cell divisions in the developing mouse cortex and promotes intermediate progenitor cell fate. We carry out RNA immunoprecipitation with a Stau2 specific antibody, followed by microarray analysis to identify Stau2 assoicated RNAs that may be shuttled asymmetrically into one daughter cell thus affecting cell fate.
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Project description:Differential gene expression of cerebral cortex might be responsible for distinct neurovascular developments between different mouse strains We used Affymetrix microarray to explore the global gene expression patterns of mouse cerebral cortex of different mouse strains at two developmental stages Cerebral cortex from two mouse strains [C57BL/6J(B6) and C3H/J (C3H)] at post-natal day 1 (p1) and post-natal 11 weeks (11 wk) were harvested for microarray experiments
2013-10-21 | E-GEOD-46443 | biostudies-arrayexpress
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
Project description:Differential gene expression of cerebral cortex might be responsible for distinct neurovascular developments between different mouse strains We used Affymetrix microarray to explore the global gene expression patterns of mouse cerebral cortex of different mouse strains at two developmental stages
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Project description:<p><strong>BACKGROUND:</strong> The protozoan parasite Toxoplasma gondii infects and alters the neurotransmission in cerebral cortex and other brain regions, leading to neurobehavioral and neuropathologic changes in humans and animals. However, the molecules that contribute to these changes remain largely unknown.</p><p><strong>METHODS:</strong> We have investigated the impact of T. gondii infection on the overall metabolism of mouse cerebral cortex. Mass-spectrometry-based metabolomics and multivariate statistical analysis were employed to discover metabolomic signatures that discriminate between cerebral cortex of T. gondii-infected and uninfected control mice.</p><p><strong>RESULTS:</strong> Our results identified 73, 67 and 276 differentially abundant metabolites, which were involved in 25, 37 and 64 pathways at 7, 14 and 21 days post-infection (dpi), respectively. Metabolites in the unsaturated fatty acid biosynthesis pathway were upregulated as the infection progressed, indicating that T. gondii induces the biosynthesis of unsaturated fatty acids to promote its own growth and survival. Some of the downregulated metabolites were related to pathways, such as steroid hormone biosynthesis and arachidonic acid metabolism. Nine metabolites were identified as T. gondii responsive metabolites, namely galactosylsphingosine, arachidonic acid, LysoSM(d18:1), L-palmitoylcarnitine, calcitetrol, 27-Deoxy-5b-cyprinol, L-homophenylalanine, oleic acid and ceramide (d18:1/16:0).</p><p><strong>CONCLUSIONS:</strong> Our data provide novel insight into the dysregulation of the metabolism of the mouse cerebral cortex during T. gondii infection and have important implications for studies of T. gondii pathogenesis.</p>
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Project description:Cajal-Retzius cells have important role in cerebral cortex development, such as secreted Reln protein, maintain normal lays of cerebral cortex. To explore novel secretory protein of Cajal-Retzius cells and to survey the roles of Cajal-Retzius cells in cerebral cortex development, we analyzed transcriptome profiles of 6753 single cells of the embryonic 18 days.
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