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Sample GSM8289839 Query DataSets for GSM8289839
Status Public on May 26, 2024
Title miRNA AC3
Sample type SRA
Source name liver
Organism Mus musculus
Characteristics tissue: liver
treatment: water week 22
Treatment protocol We construct two groups liver cancer mice model using CCl4, one group treated with PZH and the other not.
Growth protocol Male C57BL/6 mice (n=45, six weeks old) were randomly assigned to three groups: the CCl4-induced liver cancer group (liver cancer group), the PTH and CCl4-treated group (treatment group), and the control group (normal control group), with 15 mice per group. The mice in the normal control group received intragastric administration of double distilled water daily and intraperitoneal injections of olive oil twice a week. The liver cancer group was treated with intragastric administration of double distilled water daily and intraperitoneal injection of CCl4 twice a week. PTH was administrated intragastrically once a day for the treatment group, and CCl4 was injected intraperitoneally twice a week. In the 22nd week, we selected six mice from each group for RNA sequencing.
Extracted molecule other
Extraction protocol We extracted RNA from the mice liver tissues following the TRIzol reagent protocol provided by the manufacturer(Sigma).
After the removal of ribosomal RNA, two sequencing libraries were generated: NEBNext RNA Library Prep Kit (from NEB, USA) was used for lncRNA, circRNA, and mRNA sequencing, while the small RNA libraries were constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme #NR801) following the manufacturer's recommendations, respectively. Following the manufacturer's instructions, subsequent sequencing was performed on the Illumina HiSeq 4000 platform for paired-end 150 bp sequencing of lncRNAs, circRNAs and mRNAs, and on the Illumina NovaSeq platform for paired-end 50 bp sequencing of miRNAs.
Library strategy miRNA-Seq
Library source other
Library selection size fractionation
Instrument model Illumina HiSeq 4000
Data processing Data quality control was performed on raw RNA-sequencing results. For the mRNA and lncRNA sequencing data, we utilized the FastQC software (version 0.11.9) for initial quality checks and Cutadapt (version 4.2) software for adapter trimming. Following quality control, the sequencing reads were mapped to the mouse reference genome (Mus musculus GRCm38) using the HISAT2 software (version 2.2.1). Quantitative analysis of the RNA-Seq data was conducted using the StringTie software (version 2.1.5). The original expression profile was compared to the mouse annotation file to distinguish mRNA from lncRNA for further analysis.
For the miRNA sequencing data, quality control was performed and sequencing adapters were removed using Cutadapt software (version 4.2). After rigorous sequence filtering, target sequences within the 18 to 35 nucleotide (nt) range were selected. The distribution of these target sequences primarily fell within the 20 to 24 nt range, aligning with the typical length of microRNAs. Subsequently, the target sequences were mapped to the mouse reference genome (mm38) using Bowtie2 software (version 2.5.1). The aligned sequences were extracted and further mapped to the mouse reference microRNAs in miRbase using the Bowtie2 software (version 2.5.1). The CIRI2 software was employed for quantification and differential expression analysis of circle RNA.
Submission date May 24, 2024
Last update date May 26, 2024
Contact name Yongzhi Wang
Organization name Shanghai Jiao Tong University
Street address Huashan Road 1954
City Shanghai
State/province Shanghai
ZIP/Postal code 200030
Country China
Platform ID GPL21103
Series (2)
GSE268337 Transcriptome Analysis Reveals Potential Protective Effects and Biomarkers of Pien Tze Huang on CCl4-induced Liver Cancer (miRNA)
GSE268338 Transcriptome Analysis Reveals Potential Protective Effects and Biomarkers of Pien Tze Huang on CCl4-induced Liver Cancer
BioSample SAMN41528077
SRA SRX24696605

Supplementary data files not provided
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Raw data are available in SRA

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