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Sample GSM4946296 Query DataSets for GSM4946296
Status Public on Sep 22, 2023
Title Liver HFD Vehicle 705
Sample type SRA
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6N
genotype: PXR deficient
diet: High-fat diet (HFD)
treatment: intraperitoneal 30% DMSO in corn oil for four days once a day
tissue: Liver
Treatment protocol Obese mice were treated with PCN (50 mg/kg intraperitoneally) or vehicle for four days once a day.
Growth protocol 6-week old mice were kept on regular chow or high-fat diet for 18-weeks to induce obesity and obesity-related metabolic impairments.
Extracted molecule total RNA
Extraction protocol Liver pieces were lysed to RNAzol RT (Sigma-Aldrich) and total RNA was extracted per manufacturer's protocol. Samples were DNAse treated with Rnase-free Dnase set (Qiagen)
cDNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
Data processing Base calling was done with Real-Time Analysis (RTA) software version 2.
75 base pair paired-end reads were aligned to mouse Ensembl reference genome GRCm38.95 with HISAT2
Reads per gene were counted with HTSeq
Differentially expressed genes were determined with DESeq2 using Benjamini-Hochberg corrected adjusted p-value cutoff of <0.05
Genome_build: mm10
Supplementary_files_format_and_content: .txt files which include differentially expressed genes, reads per gene in all samples and log2 fold changes.
Submission date Nov 26, 2020
Last update date Sep 22, 2023
Contact name Jukka Hakkola
Organization name University of Oulu
Department Research Unit of Biomedicine
Street address Aapistie 5
City Oulu
ZIP/Postal code 90220
Country Finland
Platform ID GPL21626
Series (1)
GSE162196 Transcriptomic effect of high-fat diet and PCN treatment on the livers of of PXR deficient mice
BioSample SAMN16926500
SRA SRX9590322

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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