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Sample GSM4054789 Query DataSets for GSM4054789
Status Public on Aug 06, 2021
Title HFD PCN 11
Sample type SRA
 
Source name HFD PCN_liver
Organism Mus musculus
Characteristics strain: C57BL/6N
diet: High-fat diet (HFD)
treatment: 50 mg/kg PCN
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 15-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
 
Description processed data file:
Chow vs HFD PCN
HFD vs HFD PCN
HFD vehicle vs HFD PCN
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 GRCm38.92 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 Aug 30, 2019
Last update date Aug 06, 2021
Contact name Jukka Hakkola
E-mail(s) jukka.hakkola@oulu.fi
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)
GSE136667 Transcriptomic effect of high-fat diet and PCN treatment on mouse liver
Relations
BioSample SAMN12661230
SRA SRX6779237

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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