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Series GSE263606 Query DataSets for GSE263606
Status Public on Jun 12, 2024
Title Gene expression data from the hippocampus of mice treated with oleacein in an in vivo model of depression induced by lipopolysaccharide (LPS)-mediated inflammation.
Organism Mus musculus
Experiment type Expression profiling by array
Summary Gene expression profiling reveals potential effects of Oleacein in promoting neurogenesis and mitigating neuroinflammation in an in vivo model of depression induced by lipopolysaccharide (LPS)-mediated inflammation
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 vivo.
 
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).
 
Contributor(s) Ferdousi F
Citation(s) 38835076
Submission date Apr 09, 2024
Last update date Jun 13, 2024
Contact name Farhana Ferdousi
E-mail(s) farhana_ferdousi24@yahoo.com
Organization name University of Tsukuba
Street address Tennodai 1-1-1
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-8575
Country Japan
 
Platforms (1)
GPL23038 [Clariom_S_Mouse] Affymetrix Clariom S Assay, Mouse (Includes Pico Assay)
Samples (6)
GSM8195187 Saline administered group_rep1
GSM8195188 Saline administered group_rep2
GSM8195189 LPS induced group_rep1
Relations
BioProject PRJNA1098249

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE263606_RAW.tar 7.1 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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