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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 26, 2024 |
| Title |
miRNA AT4 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
treatment: CCL4 week 22
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| Treatment protocol |
We construct two groups liver cancer mice model using CCl4, one group treated with PZH and the other not.
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| 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.
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| 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.
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| Library strategy |
miRNA-Seq |
| Library source |
other |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
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| 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.
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| Submission date |
May 24, 2024 |
| Last update date |
May 26, 2024 |
| Contact name |
Yongzhi Wang |
| Organization name |
Shanghai Jiao Tong University
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| Street address |
Huashan Road 1954
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200030 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN41528071 |
| SRA |
SRX24696611 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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