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Sample GSM5251827 Query DataSets for GSM5251827
Status Public on Apr 19, 2021
Title Liver_ApoE-KO_rep2
Sample type RNA
Source name 111018_osawa_06_ap4
Organism Mus musculus
Characteristics genotype: ApoE-KO 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 316.8
AFFX-BioB-M_at 597.7
AFFX-BioB-3_at 260.7
AFFX-BioC-5_at 1185
AFFX-BioC-3_at 1554.4
AFFX-BioDn-5_at 2151
AFFX-BioDn-3_at 5527.1
AFFX-CreX-5_at 16688.5
AFFX-CreX-3_at 17436.3
AFFX-DapX-5_at 6.9
AFFX-DapX-M_at 4.6
AFFX-DapX-3_at 30
AFFX-LysX-5_at 4.2
AFFX-LysX-M_at 24
AFFX-LysX-3_at 33.9
AFFX-PheX-5_at 3.2
AFFX-PheX-M_at 4.7
AFFX-PheX-3_at 23.7
AFFX-ThrX-5_at 3.3
AFFX-ThrX-M_at 10.3

Total number of rows: 45101

Table truncated, full table size 713 Kbytes.

Supplementary file Size Download File type/resource
GSM5251827_111018_osawa_06_ap4.CEL.gz 5.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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