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Status |
Public on Jun 02, 2022 |
Title |
RNA-seq analysis of mRNA profiles in the livers of Wtapflox/flox and hepatocyte-specific Wtap knockout (HKO) mice |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Purpose: The goal of this study is to compare transcriptome profilings of liver from Wtapflox/flox and hepatocyte-specific Wtap knockout (HKO) mice. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of Wtap flox/flox and Wtap-HKO mice at 8 weeks old. mRNA profiles were generated by deep sequencing using an Illumina Novaseq platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.p6) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1). Conclusion: Our study represents the first detailed analysis of hepatic mRNA profiles in Wtapflox/flox and Wtap-HKO mice at 8 weeks old, generated by RNA-seq technology. Our results showed that 3486 genes were downregulated, and 3706 genes were upregulated. Gene ontology (GO) analysis showed that downregulated genes were associated with small molecule catabolic process, fatty acid metabolic process, amino acid metabolic process, steroid metabolic process, cholesterol metabolic process, xenobiotic metabolic process, fatty acid beta-oxidation, alcohol metabolic process, and glucose metabolic process, whereas the upregulated genes were associated with wound healing, leukocyte migration, chemotaxis, and positive regulation of cytokine production.
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Overall design |
The hepatic mRNA profiles of Wtap-HKO and Wtapflox/flox mice (n=3 for each group) were generated by deep sequencing using Illumina Novaseq platform.
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Contributor(s) |
Chen Z, Li X |
Citation(s) |
35927268, 37777158 |
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Submission date |
Mar 13, 2021 |
Last update date |
Dec 05, 2023 |
Contact name |
Zheng Chen |
E-mail(s) |
chenzheng@hit.edu.cn
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Phone |
+8645186402029
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Organization name |
Harbin Institute of Technology
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Street address |
92 Xidazhijie Harbin Institute of Technology
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City |
Harbin |
State/province |
Heilongjiang |
ZIP/Postal code |
150001 |
Country |
China |
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Platforms (1) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (6)
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Relations |
BioProject |
PRJNA714238 |
SRA |
SRP310501 |
Supplementary file |
Size |
Download |
File type/resource |
GSE168850_gene_fpkm.xlsx |
7.7 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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