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| Status |
Public on Jul 19, 2023 |
| Title |
Gene expression data from diabetic human adipose-derived stem cells (d-hASC) treated with 1uM oleacein |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Gene expression profiling reveals multiple biological functions of oleacein in diabetic model.
We evaluated the effects of oleacein on diabetic human adipose-derived stem cells. We performed an untargeted whole-genome transcriptome analysis to explore functionality of oleacein in a diabetic adipose stem cell-based tool.
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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 and oleacein treated hASCs samples 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.ar space) were considered as differentially expressed genes (DEGs). The fold change value around top 500 genes (FC=1.18)were extracted and sorted in descending order, for clustering and more focused enrichment analysis.
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| Contributor(s) |
Rui W |
| Citation(s) |
37445596 |
| Submission date |
Apr 26, 2023 |
| Last update date |
Jul 20, 2023 |
| 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) |
| GPL13667 |
[HG-U219] Affymetrix Human Genome U219 Array |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA962017 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE230618_RAW.tar |
4.6 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| GSE230618_processed_data_sheets.xlsx |
1.4 Mb |
(ftp)(http) |
XLSX |
| Processed data included within Sample table |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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