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Sample GSM5251822 Query DataSets for GSM5251822
Status Public on Apr 19, 2021
Title Liver_WT_rep1
Sample type RNA
Source name 111018_osawa_01_wt1
Organism Mus musculus
Characteristics genotype: WT mouse liver with HFD
strain: C57BL/6J
age: adult
Treatment protocol For liver samples, mice were feeded with HFD or 12 weeks.
Growth protocol Maintain mice in normal circumstance (temperature and humidity). For aortic endothelial cell, primary endothalial cells were isolated from aorta of each mice, and cultured for several days.
Extracted molecule total RNA
Extraction protocol For liver sample, total RNA was extracted using RNeasy (QIAGEN) according to the manufacturer's instructions. For aorta sample, Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430.2.0 Array.
Scan protocol GeneChips Scanner 3000 (Affymetrix)
Data processing The data were analyzed with GeneSpringGX (Version12.5) using Affymetrix default analysis settings and global scaling as normalization method, and Transcriptome Analysis Console (TAC) software. For global normalization, the average signal in the array was set to 100
Submission date Apr 18, 2021
Last update date Apr 19, 2021
Contact name Takashi Minami
Organization name Kumamoto University
Street address 2-2-1, Honjo
City Kumamoto
ZIP/Postal code 860-0811
Country Japan
Platform ID GPL1261
Series (1)
GSE172283 Loss of Down syndrome critical region-1 leads to cholesterol metabolic dysfunction that exaggerates hypercholesterolemia in ApoE-null background

Data table header descriptions
VALUE MAS5.0 signal intensity with target intensity=100 (Liver), and RMA (Aorta)

Data table
AFFX-BioB-5_at 422.7
AFFX-BioB-M_at 863.1
AFFX-BioB-3_at 437.9
AFFX-BioC-5_at 1477.6
AFFX-BioC-3_at 2047.8
AFFX-BioDn-5_at 2698.2
AFFX-BioDn-3_at 6511.9
AFFX-CreX-5_at 18347.9
AFFX-CreX-3_at 19497.2
AFFX-DapX-5_at 4.4
AFFX-DapX-M_at 12.9
AFFX-DapX-3_at 36.5
AFFX-LysX-5_at 3.7
AFFX-LysX-M_at 18.5
AFFX-LysX-3_at 18.9
AFFX-PheX-5_at 5.3
AFFX-PheX-M_at 7.2
AFFX-PheX-3_at 7.7
AFFX-ThrX-5_at 31.4
AFFX-ThrX-M_at 22.7

Total number of rows: 45101

Table truncated, full table size 712 Kbytes.

Supplementary file Size Download File type/resource
GSM5251822_111018_osawa_01_wt1.CEL.gz 5.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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