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| Status |
Public on Jun 24, 2024 |
| Title |
Gene expression data from 1 year old SAMP8 mouse brain cortex after 5 mg/kg daily oral administration of TCQA for 1 month |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Gene expression profiling study of cognitive-enhancing effect of TCQA in the senescence-accelerated mouse prone 8 (SAMP8) model of aging and Alzheimer’s disease
We used microarrays to detail the global gene expression underlying the mechanism of TCQA in SAMP8 mice brains
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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 TCQA-treated SAMP8 mouse brain cortex 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 (Mouse; 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) |
Chen A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jun 26, 2023 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Ashley Chen |
| E-mail(s) |
ashleychen2009@gmail.com
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| Organization name |
University of Tsukuba
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| Street address |
1 Chome-1-1 Tennodai
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| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8577 |
| Country |
Japan |
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| Platforms (1) |
| GPL23038 |
[Clariom_S_Mouse] Affymetrix Clariom S Assay, Mouse (Includes Pico Assay) |
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| Samples (4)
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| GSM7510277 |
SAMP8 mouse brain after TCQA treatment_rep1 |
| GSM7510278 |
SAMP8 mouse brain after TCQA treatment_rep2 |
| GSM7510279 |
SAMP8 mouse brain control_rep1 |
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| Relations |
| BioProject |
PRJNA987692 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE235836_RAW.tar |
5.1 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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