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Analysis of the liver transcriptome from wild-type and Gpr151 knock-out mice

ABSTRACT: Purpose: The goal of this study is to identify genes and molecular pathways whose expression is altered in the livers of Gpr151 knock-out (KO) mice compared to Gpr151 wild-type (WT). Methods: Total RNA was isolated from livers of fasted (5h) 16-week-old male mice. Deep sequencing of RNA from three wild-type and three knock-out mice was done using the mRNA-Seq pipeline at Novogene. The sequence reads that passed quality filters were aligned to the mouse GRCm38.p6 genome using STAR 2.6.1d. Differential expression testing was conducted using DESeq2. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome (build mm10) and identified 54,532 transcripts in the livers of Gpr151 WT and KO mice. RNA-seq data identified 79 transcripts which were significantly upregulated in KO (p-adj < 0.05, log2FoldChange>1) and 338 transcripts which were significantly downregulated (p-adj<0.05, log2FoldChange<-1) in KO. Conclusions: Our study represents the first detailed analysis of the liver transcriptome of Gpr151 KO mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE196535 | GEO | 2022/10/14

REPOSITORIES: GEO

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Project description:Purpose: The goals of this study are to examine how maternal exposure to oxycodone affects the global transcriptome and histological structure of the mouse placenta at 12.5 dpc of pregnancy.retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: A high throughput RNA sequencing method was used to examine the global transcriptomic changes affected by oxycodone in male and female conceptuses. Histomorphometrics were used to assess the various regions of the placenta, namely the labyrinth, spongiotrophoblast, and parietal trophoblast giant cell (pTGC) region. The open-sourced software, weighted correlation network analysis (WGCNA) was used to link gene expression changes and histological (phenotypic) changes. Results: Using an optimized data analysis workflow, we mapped over 40 million sequence reads per sample to the mouse genome (build grcm38). An average of 95.6% of reads (38.7 million) was mapped with HISAT2 workflow. We identified 12,138 transcripts in the placenta of saline control and oxycodone mice with featureCounts workflow. One hundred eighty-eight transcripts showed differential expression between the OXY male vs. CTL male placenta, with a log2Foldchange ≥1 and p value <0.05. Fifty-eight transcripts showed differential expression between the OXY female vs. CTL female placenta, with a log2Foldchange ≥1 and p value <0.05. Hierarchical clustering of differentially expressed genes uncovered several genes that may contribute to placenta function. Conclusions: Our study represents the first detailed analysis of placental transcriptomes in oxycodone-exposed mice, with biologic replicates, generated by RNA-seq technology. The data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that oxycodone exposure changed transcriptome characterization and these changes were associated with placenta histological features.

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Analysis of the liver transcriptome from wild-type and Gpr151 knock-out mice

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