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Series GSE235837 Query DataSets for GSE235837
Status Public on Jun 24, 2024
Title Gene expression data from 1 year old SAMR1 mouse brain cortex after 5 mg/kg daily oral administration of TCQA for 1 month
Organism Mus musculus
Experiment type Expression profiling by array
Summary Gene expression profiling study of normally-aging SAMR1 mice brain cortex with TCQA treatment
We used microarrays to detail the global gene expression of SAMR1 mouse brain with TCQA treatment as a control for the senescence-acCELerated mouse prone 8 (SAMP8) model of aging mice
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 SAMR1 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).
Contributor(s) Chen A
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Submission date Jun 26, 2023
Last update date Jun 24, 2024
Contact name Ashley Chen
Organization name University of Tsukuba
Street address 1 Chome-1-1 Tennodai
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-8577
Country Japan
Platforms (1)
GPL23038 [Clariom_S_Mouse] Affymetrix Clariom S Assay, Mouse (Includes Pico Assay)
Samples (4)
GSM7510281 SAMR1 mouse brain after TCQA treatment_rep1
GSM7510282 SAMR1 mouse brain after TCQA treatment_rep2
GSM7510283 SAMR1 mouse brain control_rep1
BioProject PRJNA987691

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE235837_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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