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Sample GSM5691156 Query DataSets for GSM5691156
Status Public on Nov 01, 2022
Title liver, NC2
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: liver
age: 8 weeks
treatment: control
Treatment protocol Dexmedetomidine 25 μg.kg-1 was injected intraperitoneally 30 minutes before a 70% hepatectomy performed in mice.
Extracted molecule total RNA
Extraction protocol Liver samples were obtained after 48 hours of hepatectomy.Total RNA was extracted from mouse liver tissue (n=3) using Trizol Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and RNA integrity (RIN>=6.5 & 28s/18s>=1.0) verified using an Agilent Bioanalyzer 4200 (Agilent technologies, Santa Clara, CA, US).
RNA sequencing libraries were prepared with the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611). Paired-end sequencing was completed using a Novaseq 6000 by Jiangxi HaploX Biotechnology Co., Ltd (China). Low-quality sequences and adapters were filtered by Fastp software and the clean reads mapped to the reference genome of the Mus musculus (house mouse) using HISAT2 v2.1.0.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description saline2
Data processing Qubit3.0/ Nanodrop used for basecalling.
RNA sequencing libraries were prepared with the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611). Paired-end sequencing was completed using a Novaseq 6000 by Jiangxi HaploX Biotechnology Co., Ltd (China). Low-quality sequences and adapters were filtered by Fastp software and the clean reads mapped to the reference genome of the Mus musculus (mmu10) using HISAT2 v2.1.0.
HISAT2 uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a wholegenome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments.FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups (no replicats) was performed using the EdgeR R package (1.20.0).
Genome_build: mmu10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Nov 15, 2021
Last update date Nov 01, 2022
Contact name Liqun Yang
Organization name Shanghai Jiaotong University School of Medicine
Street address No 160, Pujian road
City Shanghai
ZIP/Postal code 200217
Country China
 
Platform ID GPL24247
Series (1)
GSE188867 Next generation gene sequencing facilitates transcriptome analysis of liver tissue in dexmedetomidine-treated liver resection model mice
Relations
BioSample SAMN23167385
SRA SRX13143066

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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