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Sample GSM4231701 Query DataSets for GSM4231701
Status Public on Dec 22, 2022
Title DECB-4
Sample type RNA
 
Source name liver organization,35d,0.08mL/20g/d,replicate 1
Organism Mus musculus
Characteristics tissue: liver
gender: male
Treatment protocol After they were acclimated to the laboratory environment for 35d, 24 male mice were randomly divided into 2 groups: blank control group (CON), DECB group, 12 mice in each group. Mice in the CON group were given normal saline (0.08mL/20g), those in the DECB group were given DECB (0.08mL/20g) intragastrically once daily continuously for 35d.
Extracted molecule total RNA
Extraction protocol The total liver RNA was extracted with Trizol reagent (Invitrogen, Gaithersburg, MD, USA) and the mRNA was purified according to the instructions of RNeasy mini kit (Qiagen, Valencia, CA, USA). RNA samples were assessed for RNA integrity, inhibitor and DNA contamination by referring to the kit instructions. The quality of mRNA was detected by agarose gel electrophoresis, and the content was determined by UV spectrophotometer.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 700μL RNA using the RNeasy Mini Kit (Qiagen p/n 74104) according to the manufacturer's instructions, followed by RNAeasy column purification. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
 
Hybridization protocol 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
Scan protocol The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
Description Gene expression after 30d in mouse liver
Data processing Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.
 
Submission date Dec 23, 2019
Last update date Dec 22, 2022
Contact name guangyu xu
E-mail(s) xuguangyu2005@163.com
Organization name College of Pharmacy, Beihua University
Street address Binjiang Road 3999,jilin city,132013
City jilin city
ZIP/Postal code +860432
Country China
 
Platform ID GPL11202
Series (1)
GSE142545 Effects of deproteinized extract of calf blood on the energy metabolism of acute hypoxia model mice and its targets

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_55_P1989846 9.42247
A_55_P1991598 2.3316576
A_55_P2022211 7.831416
A_55_P1980764 6.529971
A_55_P1964375 8.99106
A_51_P128876 11.3296385
A_55_P2121042 4.4150515
A_52_P219230 2.5762203
A_51_P207591 5.092588
A_55_P2131920 7.8673797
A_55_P2404223 4.522872
A_55_P2101944 17.23573
A_52_P358860 6.6299205
A_51_P119031 7.991592
A_51_P309854 2.3510444
A_51_P343900 10.457519
A_51_P234359 7.6356325
A_51_P487813 7.9514303
A_52_P613977 7.8984275
A_55_P1957209 3.8356037

Total number of rows: 39483

Table truncated, full table size 896 Kbytes.




Supplementary file Size Download File type/resource
GSM4231701_DECB1.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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