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Sample GSM4225728

Query DataSets for GSM4225728

Status

Public on Dec 15, 2022

Title

TSD2

Sample type

SRA

Source name

Liver tissue

Organism

Sus scrofa

Characteristics

breed: Chinese Tibetan Pigs
tissue: liver
age: 3–4 months old
treatment: TP 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