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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 01, 2022 |
| Title |
liver, NC1 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: liver
age: 8 weeks
treatment: control
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| Treatment protocol |
Dexmedetomidine 25 μg.kg-1 was injected intraperitoneally 30 minutes before a 70% hepatectomy performed in mice.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
saline1
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| 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
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| Submission date |
Nov 15, 2021 |
| Last update date |
Nov 01, 2022 |
| Contact name |
Liqun Yang |
| Organization name |
Shanghai Jiaotong University School of Medicine
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| Street address |
No 160, Pujian road
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| City |
Shanghai |
| ZIP/Postal code |
200217 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE188867 |
Next generation gene sequencing facilitates transcriptome analysis of liver tissue in dexmedetomidine-treated liver resection model mice |
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| Relations |
| BioSample |
SAMN23167384 |
| SRA |
SRX13143065 |
| 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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