Ontology highlight
ABSTRACT:
PROVIDER: PRJNA745214 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15090436.fastq.gz | Fastqsanger.gz | |||
| SRR15090437.fastq.gz | Fastqsanger.gz | |||
| SRR15090438.fastq.gz | Fastqsanger.gz | |||
| SRR15090439.fastq.gz | Fastqsanger.gz | |||
| SRR15090440.fastq.gz | Fastqsanger.gz |
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Project description:To identify high-confidence NMD targets in mouse N2A neuroblastoma cells, we used our established transcriptome-wide RNA sequencing (RNA-seq) methodologies. Through parallel analyses of RNA-seq upon UPF1-knockdown (KD) and RNA immunoprecipitation (RIP-seq) footprinting of p-UPF1-bound RNAs, we identified 1027 high-confidence neuronal NMD targets.
2021-10-25 | GSE180134 | GEO
Project description:To identify high-confidence NMD targets in mouse N2A neuroblastoma cells, we used our established transcriptome-wide RNA sequencing (RNA-seq) methodologies. Through parallel analyses of RNA-seq upon UPF1-knockdown (KD) and RNA immunoprecipitation (RIP-seq) footprinting of p-UPF1-bound RNAs, we identified 1027 high-confidence neuronal NMD targets.
2021-10-25 | GSE180136 | GEO
Project description:The roles of histone demethylase KDM7 in gene expression were analyzed by gene expression profiling experiments with mouse neuroblastoma cell line Neuro2A. Keywords: mouse neuroblastoma, Neuro2A, gene expression profiling, microarray, Affimetrix M430 2.0 chip In order to examine the effect of KDM7 in gene expression, we generated stable KDM7 knockdown cell lines in mouse neuroblastoma cell line Neuro2A. Total RNAs were extracted from 5 cell lines (parental cells: Neuro2A, empty vector: Neuro2A transfected with empty vector, EGFP KD: Neuro2A transfected with vector for EGFP knock down, KDM7 KD1: Neuro2A transfected with vector 1 for KDM7 knock down, and KDM7 KD2: Neuro2A transfected with vector 2 for KDM7 knock down) and analyzed for gene expression profiles using Affymetrix platform.
2010-03-06 | E-GEOD-17494 | biostudies-arrayexpress
Project description:The roles of histone demethylase KDM7 in gene expression were analyzed by gene expression profiling experiments with the mouse neuroblastoma cell line Neuro2A.
2010-03-01 | GSE17494 | GEO
Project description:The upstream stimulating factors (USFs) USF1 and USF2 are ubiquitously expressed transcription factors characterized by a conserved basic helix-loop-helix leucine zipper DNA-binding domain. They form homo- or heterodimers and recognize E-box motifs to modulate gene expression. They are known to regulate diverse cellular functions including the cell cycle, immune response and glucose-lipid metabolism, but their roles in neuronal cells remain to be clarified. Here, we performed chromatin immunoprecipitation of USF1 from mouse brain cortex preparations. Subsequent promoter array analysis (ChIP-chip) indicated that USF1 exclusively bound to the CACGTG E-box motifs in the proximal promoter regions. Importantly, functional annotation of the USF1-binding targets revealed an enrichment of genes related to lysosomal functions. Gene expression arrays using a neuronal cell line subsequently revealed that knockdown of USFs deregulated lysosomal gene expression. Altered expression was validated by quantitative RT-PCR, supporting the conclusion that USFs regulate lysosomal gene expression. Furthermore, USFs knockdown slightly increased LysoTracker staining, implying a role for USFs in modulating lysosomal homeostasis. Together, our comprehensive, genome-scale analyses identified lysosomal genes as targets of USFs in neuronal cells, suggesting a potential additional pathway of lysosomal regulation. Gene expression profiling of neuro2a cells knocking down USFs. To screen USFs-downstream genes, mouse neuro2a cells were transfected with vectors for USFs miR RNAi or an empty vector, and then subjected to microarray analysis using Affymetrix Mouse Gene 1.0 ST Array.
2016-01-08 | E-GEOD-76615 | biostudies-arrayexpress
Project description:Voltage gated calcium channels play a central role in regulating the electrical and biochemical properties of neurons and muscle cells. Cells coordinate the expression of voltage gated calcium channels with the expression of other proteins that regulate membrane potential and calcium homeostasis. We report that the C-terminus of CaV 1.2, an L-type calcium channel (LTC) contains a C-terminal fragment that translocates to the nucleus and regulates transcription. This calcium channel associated transcription factor (CCAT) associates with transcriptional co-regulators such as p54nrb/NonO and binds to endogenous promoters. CCAT regulates the expression of gap junctions, sodium calcium exchangers, NMDA receptors, potassium channels and other proteins that regulate neuronal signaling. Electrical activity and developmental processes regulate the nuclear localization of CCAT, suggesting that the CCAT integrates information about the number of LTCs with information about the developmental history and electrical activity of a cell. These findings provide the first evidence that voltage gated calcium channels can directly activate transcription and suggest a novel mechanism linking voltage gated channels to the function and differentiation of excitable cells. Experiment Overall Design: The goal of these experiments was to identify the genes that are regulated by CCAT, a novel transcription factor derived from the C-terminus of CaV1.2. Neuro2A neuroblastoma cells were transfected with the last 503 AA of CaV1.2 which is full length CCAT (CCAT FL) or with the last 280 AA of CaV1.2, a form of CCAT that lacks the transcriptional activation domain (CCAT DTA). The mRNA from either CCAT FL or CCAT DTA expressing cells was hybridized to Agilent mouse genome microarrays along with mRNA from untransfected neuro2A cells (CCAT FL or DTA A series). Subsequent investigation revealed that transfection with the PA1 plasmid by itself increases the expression of some genes. To control for this effect we compared Neuro2A cells transfected with full length CCAT (in PA1) with Neuro2A cells transfectected with PA1 alone (CCAT FL B series). The microarray data was analyzed with the Rossetta Luminator gene expression data analysis system.
2008-06-12 | E-GEOD-4180 | biostudies-arrayexpress
Project description:In this study, we analyzed the DNA methylation levels of 4799 IAP LTRs in three murine cell types: AB2.2 ES cells, somatic cells and a neuroblastoma cell line Neuro2A. According to the results, half of the IAP LTR retrotransposons show constant methylation patterns between the three cell types whereas the remaining half display variable levels of methylation. About half of the variably methylated IAP LTRs tend to be hypomethylated in ES cells, and nearly all of this group are hypomethylated in Neuro2A cells. Interestingly, the observed hypomethylation in both cell types occur in a non-uniform, locus-specific manner and to various degrees of severity, with some of them being easily detectible by COBRA. Overall, this study demonstrates the feasibility of HT-TREBS to study alterations in DNA methylation at retrotransposons in a locus-specific manner in multiple cell types and further suggests the potential utility of this technique in developing epigenetic biomarkers for tracking disease progression. HT-TREBS has been used with the Ion Torrent PGM platform to analyze the DNA methylation of 4799 IAP LTRs in a locus-specific manner in 3 cell types: somatic cells (previously submitted under GEO Accession GSE49222), AB2.2 ES cells and Neuro2A cells
2015-06-15 | E-GEOD-60007 | biostudies-arrayexpress
Project description:We perform Selective Ribosome Profiling (SeRP) analysis of mouse Neuro2a neuronal cultures with Ebp1-immuno-precipitation in biological duplicate to assess the translation-specific function of Ebp1
2021-03-23 | GSE157361 | GEO
Project description:To investigate a role of mKIAA genes in early stage of neurite outgrowth, in vitro time course experiment was performed using the mouse neuroblastoma Neuro2A cells and all-trans-retinoic acid. Six time points of 8 biological replicates were performed.These data were normalized by median intensities and subtracted background intensities. NOTE: Outlier involved several data were not deposited. Keywords: time-course
2005-04-28 | GSE2570 | GEO
Project description:Regulation of mRNA stability is a critical step in the control of gene expression. The nonsense mediated mRNA decay (NMD) pathway is one important mRNA stability pathway and has been shown to function in regulating a significant portion of the transcriptome. Perhaps the most significant outstanding question surrounding NMD regulation of endogenous gene expression is the identification of transcripts directly targeted by the NMD pathway versus secondary response genes, whose expression levels are dependent on the activity of direct targets. Here, we present for the first time in an intact animal, the experimental identification of direct targets of NMD. We find that most genes (74%) that are upregulated in NMD mutants appear not to be direct targets of NMD. More surprisingly, we find that the vast majority (97%) of candidate direct targets are not found to be increased in expression in a NMD mutant background. These results imply negative feedback renormalizes the levels of most direct targets of NMD, suggesting they would have been missed in previous analyses. We find that our candidate direct target genes have disproportionately long 3’ UTRs compared to non-targeted control genes. Long 3’ UTRs have been shown to target mRNAs for NMD in experimental systems, and our results imply this is the case in vivo. Our results will allow for the understanding of the function of the NMD pathway in endogenous gene regulation, during normal development, as well as in pathological states.
2013-07-01 | GSE47979 | GEO