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| Status |
Public on Jun 12, 2024 |
| Title |
Gene expression data from oleacein-treated SH-SY5Y cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Gene expression profiling reveals potential effects of Oleacein in promoting neurogenesis and mitigating neuroinflammation in SH-SY5Y cells under normal and lipopolysaccharide (LPS)-induced conditions.
We evaluated the neuroprotective effects of oleacein (OC), a rare secoiridoid derivative found in extra virgin olive oil. our goal was to explore the BDNF/TrkB neurotrophic activity of OC and subsequently assess its potential for modulating neuroinflammatory response in vitro using human neuroblastoma cells (SH-SY5Y cells).
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| Overall design |
According to the manufacturer's guide, the RNA was extracted using Isogen kit (Nip-pon Gene Co. Ltd., Japan). Then, RNA quantity and quality were determined using the NanoDrop 2000 spectrophotometer (ThermoScientific, USA). DNA microarray analysis was conducted on control, oleacein-treated, LPS induced, and oleacein+LPS treated SH-SY5Y cells using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer's instructions. In brief, complementary DNA (cDNA) was synthesized from 100 ng of RNA solutions. cRNA was synthesized from in vitro transcription of cDNA and then purified and reverse transcribed. Finally, single-stranded cDNA (ss-cDNA) was synthesized, purified, fragmented, and labeled following the manufacturer's instructions. Cartridge Array Hybridization was performed using the Clariom S array (Human; ThermoFisher Scientific) on the GeneChip™ Fluidics Station (ThermoFisher Scientific). Scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data obtained after scanning were analyzed using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific). The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space) were considered as differentially expressed genes (DEGs).
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| Contributor(s) |
Ferdousi F |
| Citation(s) |
38835076 |
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| Submission date |
Apr 09, 2024 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Farhana Ferdousi |
| E-mail(s) |
farhana_ferdousi24@yahoo.com
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| Organization name |
University of Tsukuba
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| Street address |
Tennodai 1-1-1
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| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8575 |
| Country |
Japan |
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| Platforms (1) |
| GPL23159 |
[Clariom_S_Human] Affymetrix Clariom S Assay, Human (Includes Pico Assay) |
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| Samples (8)
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| GSM8195179 |
SH-SY5Y cells incubated for 48 hours in OPTI-MEM_rep1 |
| GSM8195180 |
SH-SY5Y cells incubated for 48 hours in OPTI-MEM_rep2 |
| GSM8195181 |
SH-SY5Y cells incubated for 48 hours in OPTI-MEM and 10 µM oleacein_rep1 |
| GSM8195182 |
SH-SY5Y cells incubated for 48 hours in OPTI-MEM and 10 µM oleacein_rep2 |
| GSM8195183 |
SH-SY5Y cells treated with 5 µg/ml LPS_rep1 |
| GSM8195184 |
SH-SY5Y cells treated with 5 µg/ml LPS_rep2 |
| GSM8195185 |
SH-SY5Y cells co-treated with 10 µM oleacein and 5 µg/ml LPS_rep1 |
| GSM8195186 |
SH-SY5Y cells co-treated with 10 µM oleacein and 5 µg/ml LPS_rep2 |
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| Relations |
| BioProject |
PRJNA1098250 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE263605_RAW.tar |
7.8 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Raw data provided as supplementary file |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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