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Next Generation Sequencing of ribosome-associated RNA from mouse skeletal muscle endothelial cells after 4 week treatment with vehicle or 17β-estradiol

ABSTRACT: The study evaluated the effects of estradiol treatment on gene translation in mouse skeletal muscle microvascular endothelial cells. This was accomplished by isolating ribosomes via immunoprecipitation of a tagged ribosomal protein, followed by deep sequencing of the ribosome-associated RNA (in triplicate). The sequence reads that passed quality filters were analyzed using GO analysis.

ORGANISM(S): Mus musculus

PROVIDER: GSE179737 | GEO | 2023/06/13

REPOSITORIES: GEO

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Project description:The goals of this study is to enrich the population of ovine gonadotropes via adenovirus-mediated targeting and flow cytometry to compare NGS-derived transcriptome profiling (RNA-seq) of a gonadotrope-enriched cell population to the combined transcriptome of all anterior pituitary cells and apply enrichment method to query the transcriptome of sorted ovine pituitary cells in response to treatment with 10 nM estradiol (E2) for six hours. Methods: mRNA profiles of sheep anterior pituitary cells were generated by deep sequencing, in sextuplicates, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed at the transcript level with GSNAP, followed by featureCounts and then followed by edgeR. qRT–PCR validation was performed using SYBR Green assays. Results: About 124 million sequence reads per sample were mapped to the sheep genome (Oar v.3.1) which identified 17,082 transcripts in the pituitaries. RNA-seq data confirmed overrepresentation of genes known to be expressed in pituitary in sorted samples; 11 of genes (5 gonadotrope-specific and 6 non gonadotrope-specific) were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR. Approximately 7.2% of the transcripts showed differential expression between the sorted (gonadotropes) and unsorted (all anterior pituitary cells) pituitary cells, with a fold change ≥3 and FDR <0.05. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to gonadotrope function. 232 genes were detected as upregulated in the sorted GFP-positive cells treated with E2 (gonadotropes) and 31 were downregulated following E2 treatment with a fold change ≥1.5 and FDR <0.1. Conclusions: Our study represents the first detailed analysis of the gonadotrope transcriptome, with 6 biologic replicates, generated by RNA-seq technology. The data analysis workflows reported here should provide a framework for comparative investigations of gonadotrope expression profiles. This method was applied to determine differentially expressed genes in the sorted population of pituitary cells (gonadotropes) in response to 10 nM E2.

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Next Generation Sequencing of ribosome-associated RNA from mouse skeletal muscle endothelial cells after 4 week treatment with vehicle or 17β-estradiol

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