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Sample GSM4225719 Query DataSets for GSM4225719
Status Public on Dec 15, 2022
Title WSD2
Sample type SRA
 
Source name Liver tissue
Organism Sus scrofa
Characteristics breed: Chinese Wuzhishan Pigs
tissue: liver
age: 3–4 months old
treatment: WZSP fed a standard diet
Treatment protocol two miniature pig breeds fed either standard or a high-fat and high-cholesterol diet for 6 months
Extracted molecule total RNA
Extraction protocol Total RNA were isolated from each liver samples using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. Sequencing libraries were prepared using a mRNASeqsample preparation kit (Illumina, San Diego, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Raw sequencing data were evaluated by FAST-QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), an online bioinformatics program used to characterize quality distributions of nucleotides, position-specific sequencing qualities, GC contents, the proportions of PCR duplication, and k-mer frequencies
Raw reads after quality control testing were then mapped to the reference pig genome version 10.2 (Sscrofa 10.2), using THISAT package
The normalized expression level of each gene was measured by Fragments Per Kilobase of exon per Million Reads (FPKM).
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: 4_genes_fpkm_expression.txt
 
Submission date Dec 19, 2019
Last update date Dec 15, 2022
Contact name zhaowei cai
E-mail(s) [email protected]
Phone +86 571 86613662
Organization name zhejiang chinese medical university
Department Laboratory Animal Research Center
Street address Binwen road 548
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310053
Country China
 
Platform ID GPL22475
Series (1)
GSE142346 Hepatic transcriptome response to high dietary cholesterol intake in pig NAFLD model
Relations
BioSample SAMN13634014
SRA SRX7416744

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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