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E-MEXP-1913

ABSTRACT: Transcription profiling of human neuroblastoma cell line SH-SY5Y transfected to produce phenotypes with low, medium or high levels of beta-amyloid peptides with 40 or 42 amino acids

PROVIDER: E-MEXP-1913 | ExpressionAtlas | 2015-10-22

REPOSITORIES: ExpressionAtlas

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Transcription profiling of human neuroblastoma cell line SH-SY5Y transfected to produce phenotypes with low, medium or high levels of beta-amyloid peptides with 40 or 42 amino acids

Project description:Alzheimer's disease (AD) is characterized by massive neurodegeneration and multiple changes in cellular processes, including neurogenesis. Proteolytic processing of the amyloid precursor protein (APP) plays a central role in AD. Due to varying APP processing, several beta-amyloid peptides are generated. In contrast to the form with 40 amino acids, the variant with 42 amino acids is thought to be the pathogenic form triggering the pathophysiological cascade in AD. Here, we studied the transcriptomic response to increased or decreased Abeta42 levels generated in human neuroblastoma cells. Genome-wide expression profiles (Affymetrix)were used to analyze the cellular response to the changed Abeta42 and Abeta40-levels. Human neuroblastoma cell line SH-SY5Y is a thrice cloned (SK-N-SH -> SH-SY -> SH-SY5 -> SH-SY5Y) subline of the neuroblastoma cell line SK-N-SH which was isolated and established in 1970. This cell line has 47 chromosomes. The cells possess a unique marker comprised of a chromosome 1 with a complex insertion of an additional copy of a 1q segment into the long arm, resulting in trisomy of 1q. The cell lines used in this study are SHSY5Y transfected with the constructs pCEP-C99I45F, pCEP-C99V50F, pCEP-C99 wildtype or mock transfected with an empty vector. Independent cell clones of each transfected line were used to provide biological replicates. Overexpressed C99 I45F is intracellularly cleaved resulting in high Abeta42, but low Abeta40 levels. Overexpressed C99V50F is intracellularly cleaved resulting in low Abeta42, but high Abeta40 levels. Overexpressed C99 wildtype is intracellularly cleaved resulting in medium Abeta42 and Abeta40 levels Mock is the SHSY5Y cell line transfected with the empty vector pCEP (Invitrogen) as a negative control

2009-06-01 | E-MEXP-1913 | biostudies-arrayexpress

Profiling wt SOD versus ALS SOD1(G93A) mutant

Project description:Whole-genome profiling of SH-SY5Y cells was done on neuroblastoma SH-SY5Y stably transfected with cDNAs coding for SOD1WT or the mutant SOD1(G93A) protein.

2010-12-22 | GSE21298 | GEO

The effect of knock-down of neuroblastoma associated lncRNA on transcriptome

Project description:As part of functional characterization of neuroblastoma assocated lncRNA, we performed its knock-down in neuroblastoma cell line SH-SY5Y, which resulted in modulation of expression levels of a set of genes involved in angiogenesis and inflammation, the hallmarks of metastatic cancer. SH-SY5Y cells were transfected with non-targeting siRNA control and two siRNAs targeting lncRNA BEHOT. Two days after transfection total RNA was isolated and hybridized to microarray, each sample was done in four replicas.

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Profiling wt SOD versus ALS SOD1(G93A) mutant

Project description:Whole-genome profiling of SH-SY5Y cells was done on neuroblastoma SH-SY5Y stably transfected with cDNAs coding for SOD1WT or the mutant SOD1(G93A) protein. Five wt SOD versus five mutant SOD

2010-12-22 | E-GEOD-21298 | biostudies-arrayexpress

Protein expression in MOCK and neuronal nitric oxide synthase 1 (NOS1) transduced SH-SY5Y human neuroblastoma cells on stimulation with rapamycin or serum free starvation

Project description:Neuronal nitric oxide synthase (nNOS/NOS1) is upregulated in the aging brain and contributes to age-and stress-associated neuronal dysfunctions. To mimic this situation for the study of underlying mechanisms we generated a cell model in which human SH-SH5Y neuroblastoma cells constitutively express NOS1 at a level comparable with the rodent brain, whereas the control cells have only low levels. SH-SY5Y cells are the most widely used cell model for neurodegenerative and aging research. They were stably transduced with a lentiviral vector for NOS1 and FACS sorted. Control cells were transduced with the backbone vector, referred to as MOCK or "WT-LV205". Neuronal aging of SH-SY5Y can be imposed with a number of pharmacological, genetic or stress stimuli including retinoic acid and repeated cycles of starvation. Hence, to further challenge the cells we imposed proteostasis stress by treatment with 1 µM rapamycin for 24h or culture in serum-free medium for 24h. Control cells were cultured in full medium, which was RPMI 1640 medium supplemented with heat-inactivated 10% fetal bovine serum, 100 U/ml penicillin/streptomycin, and 2 mM glutamine. All cells were kept at 37°C in 5% CO2 atmosphere in a humidified tissue culture incubator. Rapamycin elicits mTOR dependent autophagy, whereas starvation is a stimulus for chaperone-mediated autophagy, but also affects proteolysis by the proteasome and lysosome and eventually, ER stress. During stimulation, all cells were supplemented with NOS cofactors including 10 µM NAD, 40 µM NADPH, and 100 µM tetrahydrobiopterin. The proteome data set shows nNOS/NOS1-dependent alterations of protein expression in SH-SY5Y neuroblastoma cells in full medium, on stimulation with rapamycin or exposure to serum-free starvation.

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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.

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TRPM7 maintains progenitor-like features of neuroblastoma cells

Project description:Analysis of the effect of shRNA-mediated knockdown of TRPM7 on gene expression levels in SH-SY5Y and SH-EP2 human neuroblastoma cells. Results were used for the identification of neural-crest-associated transcription factors that were affected by TRPM7 knockdown. Total RNA isolated from SH-EP2 and SH-SY5Y human neuroblastoma cells transduced with a scrambled shRNA (control) or TRPM7 shRNA, experiment performed in duplicate.

2014-12-10 | E-GEOD-64000 | biostudies-arrayexpress

H3K27me3 ChIP-seq in SH-SY5Y human neuroblastoma cell line

Project description:H3K27me3 ChIP-seq was performed on: 1) untreated SH-SY5Y human neuroblastoma cells (day 0) 2) vincristine-treated SH-SY5Y human neuroblastoma cells (7 days of treatment - day 7) 3) vincristine-treated SH-SY5Y human neuroblastoma cells (7 days of treatment + 7 days of recover - day 14)

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Whole Genome Bisulfite Sequencing (WGBS) of the SH-SY5Y human neuroblastoma cell line

Project description:WGBS was performed on: 1) untreated SH-SY5Y human neuroblastoma cells (day 0) 2) vincristine-treated SH-SY5Y human neuroblastoma cells (7 days of treatment - day 7) 3) vincristine-treated SH-SY5Y human neuroblastoma cells (7 days of treatment followed by 7 days of recovery - day 14)

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Temporal Quantitative Phosphoproteomic Profiling of SH-SY5Y and IMR-32 Neuroblastoma Cells During All-trans Retinoic Acid-Induced Neuronal Differentiation

Project description:The human neuroblastoma cell lines SH-SY5Y and IMR-32 can be differentiated into neuron-like phenotypes through treatment with all-trans retinoic acid (ATRA). After differentiation, these cell lines are extensively utilized as in vitro models to study various aspects of neuronal cell biology. However, temporal and quantitative profiling of the proteome and phosphoproteome of SH-SY5Y and IMR-32 cells throughout ATRA-induced differentiation has been limited. Here, we performed relative quantification of the phosphoproteomes of SH-SY5Y and IMR-32 cells at multiple time points during ATRA-induced differentiation. The data presented serve as a valuable resource for investigating temporal protein and phosphoprotein abundance changes in SH-SY5Y and IMR-32 cells during ATRA-induced differentiation.

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