Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression profiles of primary cortical neurons after knocking down Fus

ABSTRACT: To clarify the functional properties of FUS, we established the differentially expressed alternative exons in FUS-silenced primary cortical neurons by using exon-sensitive microarray technology. We analyzed total RNA of primary cortical neuron infected with lentivirus expressing shRNA against mouse Fus or control. RNA was harvested 11 days after transfection.

ORGANISM(S): Mus musculus

SUBMITTER: Akio Masuda

PROVIDER: E-GEOD-36153 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions.

Ishigaki Shinsuke S Masuda Akio A Fujioka Yusuke Y Iguchi Yohei Y Katsuno Masahisa M Shibata Akihide A Urano Fumihiko F Sobue Gen G Ohno Kinji K

Scientific reports 20120724

FUS is an RNA-binding protein that regulates transcription, alternative splicing, and mRNA transport. Aberrations of FUS are causally associated with familial and sporadic ALS/FTLD. We analyzed FUS-mediated transcriptions and alternative splicing events in mouse primary cortical neurons using exon arrays. We also characterized FUS-binding RNA sites in the mouse cerebrum with HITS-CLIP. We found that FUS-binding sites tend to form stable secondary structures. Analysis of position-dependence of FU ...[more]

PMID: 22829983

Similar Datasets

Expression profiles of primary cortical neurons after knocking down Cugbp1

Project description:To clarify the functional properties of Cugbp1, we established the differentially expressed alternative exons in Cugbp1-silenced primary cortical neurons by using exon-sensitive microarray technology. We analyzed total RNA of primary motor neuron infected with lentivirus expressing shRNA against mouse Cugbp1 or control. RNA was harvested 11 days after transfection.

2013-04-18 | E-GEOD-46147 | biostudies-arrayexpress

Expression profiles of primary cortical neurons after knocking down Tdp-43

Project description:To clarify the functional properties of Tdp-43, we established the differentially expressed alternative exons in Tdp-43-silenced primary cortical neurons by using exon-sensitive microarray technology. We analyzed total RNA of primary motor neuron infected with lentivirus expressing shRNA against mouse Tdp-43 or control. RNA was harvested 11 days after transfection.

2013-04-18 | E-GEOD-46146 | biostudies-arrayexpress

Expression profiles of primary cortical neurons after knocking down Tdp-43 and Cugbp1

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-18 | E-GEOD-46148 | biostudies-arrayexpress

Layer 4 Visual Cortex Star Pyramid Monocular Deprivation Microarray Study

Project description:Microarray expression profiling of manually sorted m-citirin-labeled layer 4 visual cortex star pyramid neurons from deprived and non-deprived hemispheres. Monocular deprivation by TTX-injection (at P12-13 and again at P13-14), followed by manual sorting of m-Citrin-labeled Layer 4 Visual Cortex Star Pyramid neurons in deprived and non-deprived hemispheres. RNA was extracted using PicoPure RNA Isolation Kit, reverse transcribed, and amplified using a standard T7 IVT protocol (Affymetrix Small Sample Target Labeling Assay Version II).

2014-04-12 | E-GEOD-56758 | biostudies-arrayexpress

Exon array analysis in the mouse myoblast cell line, C2C12 cells treated with control-, Cugbp1- or Mbnl1-siRNA

Project description:CUGBP1 and MBNL1 are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. Using HITS-CLIP anlysis, we found CUGBP1 and MBNL1 preferentially bind to alternatively spliced introns and exons, as well as to the 3' UTRs. To analyze more directly the role of CUGBP1/MBNL1 binding in alternative splicing, we performed exon array analysis in C2C12 cells using expression arrays. We analyzed total RNA of C2C12 cells treated with control-, Cugbp1- or Mbnl1-siRNA. RNA was harvested 48 hrs after transfection.

2012-01-03 | E-GEOD-29990 | biostudies-arrayexpress

Expression data from Drd1a and Drd2 expressing neurons in striatum and cortex, at 6 weeks and 2 years of age

Project description:We performed a study of gene expression changes that occur during mouse aging in the striatum and cortex in specific neuronal populations. Using translating ribosome afifnity purificaiton, we captured cell type-specific mRNAs from Drd1a-expressing cortical neurons, Drd1a-expressing striatal neurons, Drd2-expressing cortical neurons, and Drd2-expressing striatal neurons. 31 total samples were anlayzed. We generated the followinf pairwise comparisons: Old (2 years) vs young (6 weeks) Drd1a expressing cortical cells; old (2 years) vs young (6 weeks) Drd2 expressing cortical cells; old (2 years) vs young (6 weeks) Drd1a expressing striatal cells; old (2 years) vs young (6 weeks) Drd2 expressing striatal cells. We used a restriction of Benjamini-Hochberg FDR <0.05, and a fold-change restriction of 1.2-fold.

2014-12-13 | E-GEOD-64140 | biostudies-arrayexpress

Gene expression on in vitro T cells activated with IL-21

Project description:We have analyzed the effects of IL-21 signaling on T cell activation, IL-22 production and gut inflammation In this dataset we include the results of treating T cells with IL-21. Naïve CD4+ T cells (C57BL/6) were isolated, cultured in vitro +/- IL-21 and RNA was prepared

2014-03-04 | E-GEOD-55509 | biostudies-arrayexpress

Calcineurin/Nfatc1 links skin stem cell quiescence to the endocrine hormone prolactin

Project description:Cyclosporine A (CSA) leads to the precocious onset of hair follicle growth, which is driven by premature activation and proliferation of hair follicle stem cells. Here, we identify gene expression changes associated with CSA treatment in hair follicle stem cells prior to the onset of proliferation as a readout for the early events in stem cell actvation. Hair follicle bulge stem cells were FACS-isolated from mouse skin during the 2nd telogen. Two biological replicated were performed.

2013-09-27 | E-GEOD-51194 | biostudies-arrayexpress

Conditional knockdown of DNA methyltransferase-1 (Dnmt1) reveals a key role of retinal pigment epithelium integrity in photoreceptor outer segment morphogenesis

Project description:To explore the epigenetic contribution to retinal development, we generated conditional knockout alleles of DNA methytransferase-1 (Dnmt1) mediated by Rx-Cre in mice. The results demonstrate a unique function of DNMT1-mediated DNA methylation in controlling RPE apicobasal polarity and neural retina differentiation. Retinal samples were harvested from both Dnmt1 mutant and wt animals at embryonic day 16.5 and postnatal days 0.5, 6.5, and 10.5 for microarray analysis. Each experiment was performed with biological quadruplicates. One microgram of total RNA was used for cDNA systhesis in target molecule production.

2013-01-31 | E-GEOD-43951 | biostudies-arrayexpress

Gene expression signature of Gata6 positive epidermal cells.

Project description:To characterize gene expression in Gata6 positive epidermal cells we analyzed a Gata6 reporter mouse in which the endogenous Gata6 promoter drives expression of mTomato. We performed flow cytometry followed by transcriptome analysis. We compared four subpopulations of telogen epidermal cells: Gata6+/Itga6+ cells, Gata6+/itga6- cells, CD34+/Itga6+ cells (which are Gata6-) and all remaining Itga6+ cells (Gata6-/CD34-). The RNA was isolated from age and sex matched mice. We compared four subpopulations of telogen epidermal cells: Gata6+/Itga6+ cells, Gata6+/itga6- cells, CD34+/Itga6+ cells (which are Gata6-) and all remaining Itga6+ cells (Gata6-/CD34-). The RNA was isolated from age and sex matched mice. Three biological replicates for each cell population were analyzed

2017-05-16 | E-GEOD-62606 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data