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Series GSE168850 Query DataSets for GSE168850
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
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.
 
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.
 
Contributor(s) Chen Z, Li X
Citation(s) 35927268, 37777158
Submission date Mar 13, 2021
Last update date Dec 05, 2023
Contact name Zheng Chen
E-mail(s) chenzheng@hit.edu.cn
Phone +8645186402029
Organization name Harbin Institute of Technology
Street address 92 Xidazhijie Harbin Institute of Technology
City Harbin
State/province Heilongjiang
ZIP/Postal code 150001
Country China
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (6)
GSM5171438 FF1
GSM5171439 FF2
GSM5171440 FF3
Relations
BioProject PRJNA714238
SRA SRP310501

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Supplementary file Size Download File type/resource
GSE168850_gene_fpkm.xlsx 7.7 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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