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SiRNA knockdown of hnRNP K in human SH-SY5Y cells

ABSTRACT: siRNA knockdown of hnRNP K in human SH-SY5Y cells

PROVIDER: PRJNA718307 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14095565_1.fastq.gz	Fastqsanger.gz
	SRR14095565_2.fastq.gz	Fastqsanger.gz
	SRR14095566_1.fastq.gz	Fastqsanger.gz
	SRR14095566_2.fastq.gz	Fastqsanger.gz
	SRR14095567_1.fastq.gz	Fastqsanger.gz

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siRNA knockdown of hnRNP K in human SH-SY5Y cells

Project description:The RNA-binding protein hnRNP K was knocked down using siRNA in human SH-SY5Y. As a control, cells were treated with an siRNA against firefly luciferase.

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siRNA profiling of human SH-SY5Y cells after LSD1 knock down

Project description:To analyze the functional relevance of LSD1 in neuroblastic tumors, SH-SY5Y cells were transiently transfected with siRNA directed against LSD1 or with a scrambled control siRNA. Microarray analysis revealed changes in expression that were consistent with these observations 72 hours after LSD1 knock-down. At this time, 28 genes were significantly induced at least 1.5-fold and 29 genes were significantly repressed at least 1.5-fold. Among the 28 induced genes, 4 are markers of cytoskeletal remodelling (TNS1, TPM1, DNM2, DNAL4), indicating differentiation, and 3 (TPM1, DNM2 and SHANK2) are functionally linked to neurite dynamics and synaptic trafficking. TaqMan quantitative RT-PCR confirmed the expression changes detected via microarray analysis for LSD1, DNAL4, DNM2, TNS1 and TPM1 Experiment Overall Design: SH-SY5Y cells were transfected with siRNA directed against LSD1 or control siRNA. 2 independent transfection experiments were performed each. Reverse transcription, labelling of total RNA and subsequent hybridization to Affymetrix U133v2 chips were performed according to the manufacturerÂ´s protocols

2008-11-13 | E-GEOD-13273 | biostudies-arrayexpress

Transcriptome analysis of SH-SY5Y cells after knockdown of circSLC45A4

Project description:We perturbed the expression levels of circSLC45A4 in the human neuroblastoma cell line (SH-SY5Y) by RNAi/siRNAs. 96 h post-knockdown the cells were harvested, RNA extracted with Trizol and polyA+ libraries were generated with Illumina's TruSeq RNA Library Prep Kit v2. We find many significant changes in the transcriptomic profile after knockdown of circSLC45A4 and the induction of many genes connected to nervous system development, neuron projection development, synapse organization and cell adhesion.

2019-03-31 | GSE124001 | GEO

mRNA expression analysis of human neuroblastoma cell line SH-SY5Y treated with siCLN3 vs siCTL.

Project description:To investigate impact of CLN3 deficiency on cell signaling and metabolism, SH-SY5Y neuroblastoma cells were transiently transfected with CLN3 siRNA (siCLN3; n=3) or control siRNA (siCTL; n=3). Transcriptomes of siCTL and siCLN3 SH-SY5Y cells were determined using Affymetrix Human Genome U133 plus 2 arrays.

2023-11-15 | E-MTAB-12435 | biostudies-arrayexpress

Transcriptome analysis of SH-SY5Y and SK-N-AS neuroblastoma cells with KIT gene knockdown

Project description:The goal of this study was to identify dynamic changes in signaling pathway activities after KIT knockdown by RNAi in neuroblastoma with relatively high KIT expression (SH-SY5Y) and low expression (SK-N-AS).

2018-06-23 | GSE116175 | GEO

Transcriptome analysis of SH-SY5Y cells after knockdown of circSLC45A4

Project description:Transcriptome analysis of SH-SY5Y cells after knockdown of circSLC45A4

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Gene expression during neuronal differentiation in two subtypes of SH-SY5Y

Project description:Background: SH-SY5Y cells exhibit a neuronal phenotype when treated with all-trans retinoic acid (RA), but the molecular mechanism of activation in the signaling pathway mediated by phosphatidylinositol 3-kinase (PI3K) is not sufficiently understood. To shed new light on the mechanism, we comprehensively compared the gene expression profiles between SK-N-SH cells and two subtypes of SH-SY5Y cells (SH-SY5Y-A and SH-SY5Y-E), each of which showed a different phenotype during RA-mediated differentiation. Results: SH-SY5Y-A cells differentiated in the presence of RA, whereas RA-treated SH-SY5Y-E cells required additional treatment with brain-derived neurotrophic factor (BDNF) for full differentiation. In combination with perturbation using a PI3K inhibitor, LY294002, we identified 386 genes and categorized them into two clusters dependent on the PI3K signaling pathway during RA-mediated differentiation in SH-SY5Y-A cells. Transcriptional regulation of the gene cluster was greatly reduced in SK-N-SH cells or partially impaired in SH-SY5Y-E cells in coincidence with a defect in the neuronal phenotype of these cell lines. Additional stimulation with BDNF induced a set of neural genes which were down-regulated in RA-treated SH-SY5Y-E cells but were abundant in the differentiated SH-SY5Y-A cells. Conclusions: We identified the gene clusters controlled by PI3K- and TRKB-mediated signaling pathways during differentiation in two subtypes of SH-SY5Y cells. TRKB-mediated bypass pathway compensates for the impaired neural functions generated by defects in several signaling pathways including PI3K in SH-SY5Y-E cells. The expression profiling data are useful for further studies to elucidate the signal transduction-transcriptional network including PI3K and/or TRKB. Keywords: Cell type comparison, time course

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Project description:The SH-SY5Y Human neuroblastoma cell line was subcloned from the SK-N-SH cell line, which has been isolated from a bone marrow biopsy of a 4 year-old female patient. To examine the overall distribution of gene expression under stress condition in human neuronal cells, we investigated changes in the transcriptome profiles in the SH-SY5Y cells depleted with ERRαlpha and ERRgamma by gene knockdown. We detected changes in the expression levels for several genes.

2024-08-20 | GSE208270 | GEO

Profiling neuroblastoma SH-SY5Y with Paraquat treatment

Project description:Human SH-SY5Y neuroblastoma cells treated with paraquat, a neurotoxic herbicide which both catalyzes the formation of reactive oxygen species (ROS) and induces mitochondrial damage in animal models was profiled using Affimetrix Exon 1.0 ST GeneChips® Human SH-SY5Y neuroblastoma cells was compared with respect to Human SH-SY5Y neuroblastoma cells treated with Paraquat. Parqaut treatment was done as described by Maracchioni, A., Totaro, A., Angelini, D.F., Di Penta, A., Bernardi, G., Carri, M.T., and Achsel, T. (2007) J Neurochem 100, 142-153

2010-12-22 | E-GEOD-21305 | biostudies-arrayexpress

Expression data from BBEE-treated SH-SY5Y cell

Project description:Gene expression profiling reveals anti-inflammatory effects of BBEE on lipopolysaccharide (LPS)-induced Human neuronal SH-SY5Y cells We evaluated the pretreatment effect of BBEE on LPS-induced inflammation in SH-SY5Y cells. Pretreatment with BBEE could significantly attenuate nitric oxide (NO) production and LPS-induced release of inflammatory mediators in SH-SY5Ycells.

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