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Status |
Public on Dec 15, 2022 |
Title |
WSD2 |
Sample type |
SRA |
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Source name |
Liver tissue
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Organism |
Sus scrofa |
Characteristics |
breed: Chinese Wuzhishan Pigs tissue: liver age: 3–4 months old treatment: WZSP fed a standard diet
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Treatment protocol |
two miniature pig breeds fed either standard or a high-fat and high-cholesterol diet for 6 months
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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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
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Submission date |
Dec 19, 2019 |
Last update date |
Dec 15, 2022 |
Contact name |
zhaowei cai |
E-mail(s) |
[email protected]
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Phone |
+86 571 86613662
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Organization name |
zhejiang chinese medical university
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Department |
Laboratory Animal Research Center
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Street address |
Binwen road 548
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City |
Hangzhou |
State/province |
Zhejiang |
ZIP/Postal code |
310053 |
Country |
China |
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Platform ID |
GPL22475 |
Series (1) |
GSE142346 |
Hepatic transcriptome response to high dietary cholesterol intake in pig NAFLD model |
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Relations |
BioSample |
SAMN13634014 |
SRA |
SRX7416744 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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