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Transcriptomic profiling of cerebrum, liver, and muscle tissues of 50 days fetuses in response to early maternal nutrient restriction

ABSTRACT: Transcriptomic profiling of cerebrum, liver, and muscle tissues of 50 days fetuses in response to early maternal nutrient restriction

PROVIDER: PRJNA645822 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12207823_1.fastq.gz	Fastqsanger.gz
	SRR12207823_2.fastq.gz	Fastqsanger.gz
	SRR12207824_1.fastq.gz	Fastqsanger.gz
	SRR12207824_2.fastq.gz	Fastqsanger.gz
	SRR12207825_1.fastq.gz	Fastqsanger.gz

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Transcriptomic profiling of cerebrum, liver, and muscle tissues of 50 days fetuses in response to early maternal nutrient restriction

Project description:We addressed the molecular mechanisms and biological processes underlying the differences in cerebrum, liver, and muscle gene expression of 50 days fetuses in response to early maternal nutrient restriction. To this end, we employed tissue-to-tissue and tissue-specific network approaches using the genome-wide expression profile of 14 samples for two experimental conditions [Control – CON (n = 7) and 40% nutrient restriction – RES (n = 7)]. After RNA quality control, read mapping was performed with STAR aligner to the bovine ARS-UCD1.2 reference genome. Count normalization was performed by using the VST function from DESEq2. Gene networks were constructed using the PCIT algorithm, whereas differentially co-expressed genes were identified based on the R-package DGCA. Significant gene-gene co-expression was taken based on r > | 0.9| and then filtered by differentially expressed genes and transcription factors. Networks were visualized in Cytoscape, and functional analyses were carried out on Cluego and ShinyGo tools. We found that the cerebrum, liver, and muscle tissues were affected by nutrient restriction leading to differences in transcriptional regulation between CON and RES groups. Furthermore, we shed light on the nutrient-sensing pathways across tissues such as mTOR, PI3K/Akt, and insulin. This project was supported by Agriculture and Food Research Initiative Competitive Grant no. 2016-67016-24946 from the USDA National Institute of Food and Agriculture as well as the USDA-NIFA-AFRI (2018-67011-31708).

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