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Sample GSM8195179 Query DataSets for GSM8195179
Status Public on Jun 12, 2024
Title SH-SY5Y cells incubated for 48 hours in OPTI-MEM_rep1
Sample type RNA
 
Source name SH-SY5Y cells incubated for 48 hours in OPTI-MEM
Organism Homo sapiens
Characteristics cell line: SH-SY5Y
Treatment protocol Oleacein was dissolved in dimethyl sulfoxide (DMSO, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) and further diluted in serum-free Eagle's minimum essential medium (OPTI-MEM, Gibco) to achieve treatment concentration 10 µM. Twenty-four hours after seeding, the SH-SY5Y cells were incubated for 48 hours in OPTI-MEM without or with oleacein. For inflammation model, following seeding of SH-SY5Y cells in 60 mm dishes, the cells were transitioned from growth medium to OPTI-MEM and incubated for 24 hours. Subsequently, 10 µM oleacein and 5 µg/ml LPS (FUJIFILM Wako Pure Chemical Corporation) were co-administered to the cells for an additional 24 hours in OPTI-MEM.
Growth protocol SH-SY5Y cells (2 × 106 cells/5 ml growth medium) were seeded into 60 mm dishes. Twenty-four hours after seeding, the SH-SY5Y cells were incubated for 48 hours in OPTI-MEM.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA
 
Hybridization protocol The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Human; ThermoFisher Scientific).
Scan protocol Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).
Description Gene expression data from SH-SY5Y cells incubated for 48 hours in OPTI-MEM
SST-RMA
Data processing 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 background (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.
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files). filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space)
signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4)
 
Submission date Apr 09, 2024
Last update date Jun 12, 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
 
Platform ID GPL23159
Series (1)
GSE263605 Gene expression data from oleacein-treated SH-SY5Y cells

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 6.0832
AFFX-BkGr-GC04_st 5.3078
AFFX-BkGr-GC05_st 5.10035
AFFX-BkGr-GC06_st 5.08651
AFFX-BkGr-GC07_st 4.87413
AFFX-BkGr-GC08_st 4.53001
AFFX-BkGr-GC09_st 4.32004
AFFX-BkGr-GC10_st 4.06927
AFFX-BkGr-GC11_st 4.06254
AFFX-BkGr-GC12_st 3.98638
AFFX-BkGr-GC13_st 3.90569
AFFX-BkGr-GC14_st 3.78665
AFFX-BkGr-GC15_st 3.63219
AFFX-BkGr-GC16_st 3.67975
AFFX-BkGr-GC17_st 3.6634
AFFX-BkGr-GC18_st 3.70562
AFFX-BkGr-GC19_st 4.3031
AFFX-BkGr-GC20_st 4.32704
AFFX-BkGr-GC21_st 4.36254
AFFX-BkGr-GC22_st 4.3171

Total number of rows: 24351

Table truncated, full table size 635 Kbytes.




Supplementary file Size Download File type/resource
GSM8195179_Control_1.CEL.gz 804.6 Kb (ftp)(http) CEL
GSM8195179_Control_1.chp.gz 169.6 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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