DYX1C1 perturbation experiments in the SH-SY5Y cell line
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Morana Vitezic
PROVIDER: E-MTAB-1128 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Investigation of whole genome expression in SH-SY5Y cells transfected Elk-1-VP16 cells compared to pCDNA3 transfected cells as a control.
2021-02-28 | E-MTAB-9938 | biostudies-arrayexpress
Project description:We conducted a proof-of-concept experiment to explore the possibility of using gene expression-based high throughput screening (GE-HTS) to find inhibitors of a signaling cascade, using platelet derived growth factor receptor (PDGFR) signaling as the example. To define ERK/PDGFR activation signature, we performed gene expression profiling using Affymetrix U133A arrays 0.5-4 hours following PDGF stimulation, thereby identifying those genes whose expression is correlated with PDGFR activity. In order to identify the component of the gene expression signature that was attributable to ERK activation by PDGFR (as opposed to other pathways downstream of PDGFR), we also pretreated the cells will the ERK inhibitors U0126 and PD98059, and repeated the gene expression profiling studies. Experiment Overall Design: To define ERK/PDGFR activation signature, SH-SY5Y cells were grown to confluence and starved overnight in serum-free medium in order to silence any sustained effects from growth factor signaling. Prior to induction with 50ng/ml PDGF, cells were treated with pathway inhibitors 74 mM Apigenin or 50 mM U0126, or with DMSO (carrier) for 60 minutes. Total RNA was isolated 30 minutes after PDGF addition. Experiments were performed in duplicate. The RNA was processed and hybridized with Affymetrix U133A GeneChips.
2008-04-06 | E-GEOD-7403 | biostudies-arrayexpress
Project description:This experiment captures expression over 60,000 well-annotated RefSeq human transcripts over RNA samples from SH-SY5Y neuroblastoma cells transfected with human and non-human primate microRNA mimic variants of miR-299-3p, miR-503-3p, miR-508-3p and miR-541-3p, as well as a RNA duplex negative control (C2 mimic, Dharmacon).
2016-04-03 | E-MTAB-3617 | biostudies-arrayexpress
Project description:MicroRNA (miRNA) has been highlighted in pathogen-host interactions, however, little is known about roles of miRNAs in neurological pathogenesis of human enterovirus 71 (HEV71) infections. In this study, the comprehensive miRNA expression profiling in HEV71-infected human neuroblastoma SH-SY5Y cells were performed to identify cellular miRNAs response to HEV71. A total of 69 miRNAs were differentially expressed in HEV71-infected SH-SY5Y cells compared to non-infected cells. These findings provide new information on the miRNA and mRNA profiles in HEV71 infection, which may serve as a basis for further investigation into the biological functions of miRNAs in the neurological pathogenesis of HEV71 infections. Human neuroblastoma SH-SY5Y cells were infected with HEV71. After infection, the cells were harvested and extracted total RNA for miRNA profiling by hybridization on Affymetrix microarrays. A total of 69 miRNAs were differentially expressed inHEV71-infected SH-SY5Y cells compared to non-infected cells.
2014-07-31 | E-GEOD-45816 | biostudies-arrayexpress
Project description:Today, the pathogenesis of human enterovirus type 71 (HEV71) infection in human central neural system remains unclear. HEV71 is the major pathogen of hand-foot-and-mouth disease (HFMD), and has been associated with severe neurological disease and even death in infants and young children. We employed the human whole genome microarray analyze the transcriptome profiling inhuman neuroblastoma cells SH-SY5Y infected with HEV71. The results showed that HEV71 infection lead to altered expression of 161 human mRNAs including 74 up-regulated genes and 87 down-regulated genes. Then we found that the possible roles of the differentially regulated mRNAs in selected pathways including cell cycle/proliferation, apoptosis, and cytokine/chemokine responses by Bioinformatic analysis. Furthermore, we validated the microarray results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about host response to HEV71 infection in human neuroblastoma cells, and this finding will help to understand the pathogenesis of HEV71 infection and virus-host interaction. Total RNA of cells infected with HEV71 was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each pooling RNA sample separately on the GeneChip_ Porcine Genome Array (Affymetrix) at CapitalBio Corporation (Beijing, China) in which GeneChip microarray service was certificated by Affymetrix.
2013-10-31 | E-GEOD-45589 | biostudies-arrayexpress
Project description:Today, the pathogenesis of human enterovirus type 71 (HEV71) infection in human central neural system remains unclear. HEV71 is the major pathogen of hand-foot-and-mouth disease (HFMD), and has been associated with severe neurological disease and even death in infants and young children. We employed the human whole genome microarray analyze the mRNA profiling in human neuroblastoma cells SH-SY5Y infected with HEV71 after transfection. Firstly, SH-SY5Y cells were transfected wtih miR-1246 inhibitor and negtive control respectively using HiPerFect Transfection Reagent according to the manufacturer’s instructions. Then the cells were infected with HEV71 after transfection. After 12 hours infection, the cells were harvested to microarray analysis. The results showed the altered expression of mRNAs including up-regulated genes and down-regulated genes. Overall, this finding will help to understand the functional genes in HEV71-infected human neuroblastoma cells and miR-1246-virus-host interaction. SH-SY5Y cells were transfected wtih miR-1246 inhibitor and negtive control respectively using HiPerFect Transfection Reagent according to the manufacturer’s instructions. Then the cells were infected with HEV71 after transfection. After infection, the cells were harvested to microarray analysis. Total RNA of cells infected with HEV71 was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each pooling RNA sample separately on the GeneChip_ Porcine Genome Array at CapitalBio Corporation (Beijing, China).
2014-07-31 | E-GEOD-45817 | biostudies-arrayexpress
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. Experiment Overall Design: Human neuroblastomas, SK-N-SH (HTB-11) and SH-SY5Y-A cells (CRL-2266) were obtained from the American Type Culture Collection (ATCC). We also obtained SH-SY5Y-E cells (EC94030304) from the European Collection of Cell Cultures (ECACC). Tissue culture cells were maintained in D-MEM/F12 1:1 mixture supplemented with 15% FBS (Fetal Bovine Serum) and 1% NEAA (Non-essential amino acid) in a 5% CO2 humidified incubator at 37oC. The culture medium was changed twice a week. For the RA-inducible experiment, random culture cells from two clone subtypes of SH-SY5Y and SK-N-SH were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences, Billerica, MA, USA) for 1 day and then transferred to a medium containing 10 μM of RA in the presence or the absence of LY294002 (10μM) for five days. For BDNF-induced sequential differentiation of the SH-SY5Y-E strain, cells were washed with D-MEM/F12 twice after five days in the presence of RA and then incubated with 50 ng/ml of BDNF in D-MEM/F12 without serum for three days.
2009-09-04 | E-GEOD-9169 | biostudies-arrayexpress
Project description:S-palmitoylation is the covalent attachment of palmitic acid to cysteine residues through a thioester bond. S-palmitoylation is highly abundant in neurons, where it plays a fundamental role in neuronal development. In addition, S-palmitoylation is associated with many neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and Huntington's disease. However, knowledge of S-palmitoylation in neurodevelopment is limited due to technological challenges in analysing this highly hydrophobic modification of proteins. Here, we use two orthogonal methods, acyl-biotin exchange and lipid metabolic labelling, to identify S-acylated proteins and sites in neuronal cells. We identified 650 S-palmitoylated proteins by both methods, including proteins that are well-known for their role in neuronal differentiation. Importantly, significant changes in the abundance of S-palmitoylated proteins were detected during neuronal differentiation. Overall, the combination of methods described here provides the advantage of cross-validation of the identified S-palmitoylated proteins and should be used further to study S-palmitoylation in the central nervous system to understand physiology and neurodegenerative diseases.
2023-10-24 | PXD040613 | Pride
Project description:Stable ETV5 knockdown SH-SY5Y were used to investigate the role of ETV5 in vitro and in vivo. Libraries for mRNA sequencing were prepared using the TruSeq stranded mRNA sample prep kit (Illumina), involving polyA-selection, fragmentation, adapter ligation, reverse transcription and PCR amplification. Libraries were quantified using the Qubit 2.0 Fluorometer prior to sequencing with read length of 75 bp on a NextSeq 500 sequencer (Illumina). On average 24.7 M high-quality reads were generated per sample, with a minimal read count of 20.0 M reads for sample 2015_027_009 (sample L105). For each sample, gene-level read counts and KPKM-values were generated with Sailfish (Patro et al. 2014). Read counts are the number of reads overlapping a given feature such as a gene. KPKM-values (K-mers Per Kilobase of exon per Million reads) represent read counts normalized for sequencing depth and transcript length. KPKM-values allow you to compare genes across and within samples.
2020-05-01 | E-MTAB-6713 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in SH-SY5Y cells transfected pCDNA3-Pea3, pCDNA3-Erm, and pCDNA3-Er81 cells compared to pCDNA3 transfected cells as a control.
2020-10-28 | E-MTAB-8473 | biostudies-arrayexpress