|
| Status |
Public on Jun 24, 2024 |
| Title |
SAMR1 mouse brain after TCQA treatment_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
SAMR1 mice brain cortex after oral administration of TCQA
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Brain cortex
|
| Treatment protocol |
The 11 month old mice received 5 mg/kg daily oral administration of TCQA for 1 month. MilliQ water was administered for control groups.
|
| Growth protocol |
7-month-old male SAMR1 mice were housed individually in cages at the Gene research center at the University of Tsukuba for 4 months.
|
| 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, Mouse; ThermoFisher Scientific).
|
| Scan protocol |
Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).
|
| Description |
Gene expression data from SAMR1 mice brain cortex after oral administration of TCQA for 1 month
|
| 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.
SST-RMA
|
| |
|
| Submission date |
Jun 26, 2023 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Ashley Chen |
| E-mail(s) |
ashleychen2009@gmail.com
|
| Organization name |
University of Tsukuba
|
| Street address |
1 Chome-1-1 Tennodai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8577 |
| Country |
Japan |
| |
|
| Platform ID |
GPL23038 |
| Series (1) |
| GSE235837 |
Gene expression data from 1 year old SAMR1 mouse brain cortex after 5 mg/kg daily oral administration of TCQA for 1 month |
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