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Sample GSM6330083 Query DataSets for GSM6330083
Status Public on Jul 15, 2022
Title NCO
Sample type RNA
 
Source name hippocampus, administered orally,15day
Organism Mus
Characteristics strain: Slc:ddY mice
tissue: hippocampus
gender: male
age: 6week
treatment: control
Treatment protocol After the measurement of spontaneous alternation behavior in the Y-maze experiment, mice were euthanized with CO2 gas, and decapitated. The hippocampus, which was collected from the isolated brain, was pretreated by immersion in RNAlater RNA Stabilization Reagent (RNAlater). The RNAlater-treated hippocampus was stored frozen (< -70 °C).
Growth protocol The experiment was divided into three groups: the normal control group (NCO), the Aβ25-35 injected-control group (ACO), and the Aβ25-35 injected-shochu oil group (ASO). The experimental substance was administered orally to mice for 15 days, with distilled water (the medium) given to those in the NCO and ACO groups. Shochu oil (administered to the ASO group) was administered orally at 2,000 mg/kg/day. Each mouse in the NCO group was given 5 μL of distilled water, Each mouse in the ACO and the SCO groups was intracerebroventricularly injected 5 μL (10 nmol) of the Aß25-35 solution on the 8th day after oral administration began. The Y-maze spontaneous alternation experiment was conducted on day 16. Samples for RNA extraction were derived from RNAlater-treated frozen hippocampus stored after measurement of the Y-maze spontaneous alternation (n = 10).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNAiso plus following the manufacturer’s instructions. To balance the data reproducibility and cost performance, we pooled the RNA from two mice as one set and obtained five sets from ten mice in each group. After centrifugation, the RNA was precipitated from the aqueous layer, washed, and dissolved in DNase/RNase-free distilled water. Next, the extracted total RNA liquid phase was mixed with DNase/RNase-free distilled water and purified with the RNeasy MinElute Cleanup Kit. RNA concentration and integrity were assessed by spectrophotometry and gel electrophoresis. The total RNA obtained was measured for absorbance at 260 nm and 280 nm, and the ratio of absorbance at 260 nm and 280 nm was used to assess the purity of RNA. A ratio of over 2.0 was generally accepted as “pure” for RNA. The extracted total RNA was stored frozen (< -70 °C).
Label Cy3
Label protocol Two hundred-nanogram samples of total RNA pooled in equal amounts of five samples from each group were synthesized with cDNA, Cy3-labeled cRNA, and purified using the Low Input Quick Amp Labeling Kit. The concentration of labeled cRNA and Cy3 incorporation was calculated from the absorbance at 260, 280, 550, and 320 nm, and we confirmed that the standard value (Cy3-CTP incorporation > 6 pmol/g) was reached.
 
Hybridization protocol Each labeled cRNA of 1.65 µg was fragmented using the Gene Expression Hybridization Kit and applied to the Whole Mouse Genome Microarray Ver2.0 slide for 17 h hybridization at 65 °C.
Scan protocol Gene expression analyses were performed using the array analysis software GenePix Pro. A microarray scanner GenePix 4000B, was used to produce an array image scan digitized with the array analysis software GenePix Pro.
Description hippocampus_frozen_repbM
Data processing The signal data for the features (spots of the array) were imported into GeneSpring 12.6 (Agilent Technologies, Inc.) and further analyzed with the software. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.The signal data from the arrays were normalized using the 75th percentile method, and baseline transformation was performed with the median of the control samples.
 
Submission date Jul 12, 2022
Last update date Jul 16, 2022
Contact name 超 章
E-mail(s) zhang_chau@kirishima.co.jp
Phone 07023999093
Organization name 霧島酒造株式会社
Street address 下川東4丁目28号1番
City 都城市
State/province 宮崎県
ZIP/Postal code 885-8588
Country Japan
 
Platform ID GPL11202
Series (1)
GSE208013 Ameliorative effect of the oil components derived from sweet potato shochu on impaired short-term memory in mice after amyloid ß25-35 injection

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_55_P1953439 42.8
A_55_P2002113 2980.8
A_55_P2039603 348.8
A_55_P2007575 7.8
A_55_P2135701 22.8
A_55_P2128591 89.8
A_55_P2093749 21.8
A_51_P367125 96.8
A_55_P2023424 174.8
A_52_P564951 28.8
A_52_P472324 24.8
A_55_P1998471 50.8
A_66_P103477 48.8
A_52_P433864 25.8
A_55_P2053718 2404.8
A_55_P2076545 39.8
A_55_P2024625 62.8
A_51_P452629 33.8
A_51_P249594 28.8
A_55_P1997429 172.8

Total number of rows: 475

Table truncated, full table size 8 Kbytes.




Supplementary file Size Download File type/resource
GSM6330083_NCO_raw_data.txt.gz 4.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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