Transcriptomic profiling of caruncular and cotyledonary tissues of 83 days fetuses in response to early maternal nutrient supplementation
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ABSTRACT:
PROVIDER: PRJNA694189 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13511200_1.fastq.gz | Fastqsanger.gz | |||
| SRR13511200_2.fastq.gz | Fastqsanger.gz | |||
| SRR13511201_1.fastq.gz | Fastqsanger.gz | |||
| SRR13511201_2.fastq.gz | Fastqsanger.gz | |||
| SRR13511202_1.fastq.gz | Fastqsanger.gz |
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Project description:We measured the gene expression profile of fetal liver to identify differentially expressed genes (DEG), biological processes (BP), and pathways underlying hepatic function and development in response to vitamin and mineral supplementation (VTM or NoVTM – at least 71 days pre-breeding to day 83 of gestation) and rate of weight gain (low [LG] or moderate [MG] – from breeding to day 83). The treatments were arranged as follows: (1) no vitamin and mineral supplementation and low gain (NoVTM_LG, n = 8); (2) vitamin and mineral supplementation and low gain (VTM_LG, n = 8); (3) no vitamin and mineral supplementation and moderate gain (NoVTM_MG, n = 8), and (4) vitamin and mineral supplementation and moderate gain (VTM_MG, n = 7). Crossbred Angus beef heifers (n = 35) were randomly assigned to 1 of 4 treatments in a 2 × 2 factorial design. Fetal liver was collected on day 83 ± 0.27 of gestation snap-frozen, and stored at −80 °C. After RNA quality control, read mapping was performed with STAR aligner to the bovine ARS-UCD1.2 reference genome. Strand-specific RNA libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs®, Ipswich, MA, USA). Total RNA was extracted and libraries were sequenced on the Illumina® NovaSeq 6000 platform. After RNA quality control, read mapping was performed with STAR aligner to the bovine ARS-UCD1.2 reference genome. After quality control, differential gene expression analysis was carried out using edgeR. Differentially expressed genes (DEGs) were identified after multiple testing correction of the p-values based on the Benjamini-Hochberg methodology (FDR < 0.1). Our results show that vitamin and mineral supplementation and the rate of weight gain led to differential expression of hepatic genes in all treatments. We identified 591 unique differentially expressed genes across all six VTM-gain contrasts (FDR < 0.1). Over-represented pathways were related to energy metabolism, including PPAR and PI3K-Akt signaling pathways, as well as lipid metabolism, mineral transport, and amino acid transport. Our findings suggest that periconceptual maternal nutrition affects fetal hepatic function through altered expression of energy and lipid-related genes.
2023-04-14 | GSE224419 | GEO
Project description:Transcriptomic profiling of liver tissues of 83 days fetuses in response to early maternal nutrient supplementation
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Project description:We measured the gene expression profiles of maternal (caruncular; CAR) and fetal (cotyledonary; COT) portions of the placenta to identify differentially expressed genes (DEG), biological processes (BP), and pathways underlying placental development and function in response to early maternal nutrition. To this end, we used the RNA-Seq-based differential expression analysis of bovine placental tissues. The factors examined included vitamin and mineral supplementation (VTM or NoVTM) and rate of gain (low gain – LG or moderate gain – MG). The treatments were arranged as follows: (1) no vitamin and mineral supplementation and low gain (NoVTM_LG, n = 9); (2) vitamin and mineral supplementation and low gain (VTM_LG, n = 9); (3) no vitamin and mineral supplementation and moderate gain (NoVTM_MG, n = 9), and (4) vitamin and mineral supplementation and moderate gain (VTM_MG, n = 8). On day 83 ± 0.27 of gestation the uteroplacental tissues were collected through ovariohysterectomy and the largest placentome closest to the fetus was collected. Then, maternal (CAR) and fetal (COT) portions were manually dissected, snap-frozen, and stored at −80 °C. After RNA quality control, read mapping was performed with STAR aligner to the bovine ARS-UCD1.2 reference genome. Genes with expression values lower than 1 count per million in 50% of the samples were filtered out. After filtering, the genes of CAR and COT tissues were analyzed using the DESeq2 v.1.22.1 software to identify DEGs. The DESEq2 model was used to measure the treatment effect while controlling for batch effect differences that included the surrogated variables (sva) and the heifer’s birthplace (farm of origin). Genes were identified as differentially expressed for each one of the contrasts when the adjusted p-value (padj) cutoff < 0.1 and classified as up- or down-regulated based on the sign of the log2 fold change. We identified 267 unique DEGs throughout all tissues and group contrasts. The over-represented functions are essential to fetal growth and development, and included fatty acid metabolism, hormone synthesis, nutrient transport, energy metabolism, and biosynthesis of amino acids.
2021-04-01 | GSE165378 | GEO
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).
2021-02-08 | GSE154299 | GEO
Project description:Hepatic gene expression in male fetuses from maternal nutrient restriction in mice
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Project description:Transcriptomic profiling of cerebrum, liver, and muscle tissues of 50 days fetuses in response to early maternal nutrient restriction
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Project description:Placental development is modified in response to maternal nutrient restriction (NR) resulting in a spectrum of fetal growth rates. Pregnant sheep carrying singleton fetuses and fed either 100% (n=8) or 50% (NR; n=28) of their National Research Council (NRC) recommended intake from Days 35 to 135 of pregnancy were used to elucidate placentome transcriptome alterations at both Day 70 and 135. NR fetuses were further designated into upper (NR NonSGA; n=7) and lower quartiles (NR SGA; n=7) based on Day 135 fetal weight. At Day 70 of pregnancy, there were 22 genes dysregulated between NR SGA and 100% NRC placentomes, 27 genes between NR NonSGA and 100% NRC placentomes, and 22 genes between NR SGA and NR NonSGA placentomes. These genes mediated molecular functions such as MHC class II protein binding, signaling receptor binding, and cytokine activity. Gene Set Enrichment Analysis (GSEA) revealed significant overrepresentation of genes for natural killer cell-mediated cytotoxicity in NR SGA compared to 100% NRC placentomes and alterations in nutrient utilization pathways between NR SGA and NR NonSGA placentomes at Day 70. Results identify novel factors associated with impaired function in SGA placentomes and potential for placentomes from NR NonSGA pregnancies to adapt to nutritional hardship.
2021-07-17 | GSE180182 | GEO
Project description:The aim of this study was to identify fetal adaptations to gene expression in our mouse model of intrauterine growth restriction (IUGR). Starting at E6.5, pregnant CD-1 mice received either control (ad libitum) or 70% of ad libitum food (maternal nutrient restriction [MNR]). At E18.5, fetal right liver lobes were collected from 2 pups/litter in litters with 11-15 pups. Frozen liver was homogenized for RNA isolations. Isolated RNA was sequenced on a HiSeq2500 with an average read depth of 23M reads and a range of 17-31M reads per sample. Reads were aligned to the mm9 transcriptome with Bowtie2. Normalization and differential expression was done with DESeq2, ALDex2 and EdgeR, and genes were considered in the study if they were consistent in 2 or more tools (FDR <0.1).
2019-12-17 | GSE124006 | GEO
Project description:Suboptimal intrauterine nutrition predisposes the fetus to central obesity and metabolic syndrome in adult life, suggesting nutritional programming of the fat distribution. However, the underlying mechanisms are not elucidated. We hypothesized that prenatal nutritional deprivation leads to stimulation of adipogenesis, as an adaptive mechanism, in a depot-dependent manner. The induction of adipogenesis is most enhanced in the subcutaneous lower-body depots, followed by the subcutaneous upper-body and visceral adipose tissue depots. Stimulation of adipogenesis may lead to an early consumption of the stem cell pool, and thus, may impair adipose tissue expandability postnatally, which may lead to differences in regional adipose tissue growth. We tested this hypothesis by analyzing global gene expression to identify expression patterns in subcutaneous abdominal, subcutaneous femoral, and omental adipose depots of baboon fetuses that have been altered by nutritional maternal deprivation. Adipose tissue was collected from baboon fetuses at 165 dG from mothers fed control or 30% nutrient-restricted diets (three females and one male in each group). 24 samples, each consisted of pooled total RNA from triplicate wells (6-well plate).
2011-12-16 | E-GEOD-34464 | biostudies-arrayexpress
Project description:Suboptimal intrauterine nutrition predisposes the fetus to central obesity and metabolic syndrome in adult life, suggesting nutritional programming of the fat distribution. However, the underlying mechanisms are not elucidated. We hypothesized that prenatal nutritional deprivation leads to stimulation of adipogenesis, as an adaptive mechanism, in a depot-dependent manner. The induction of adipogenesis is most enhanced in the subcutaneous lower-body depots, followed by the subcutaneous upper-body and visceral adipose tissue depots. Stimulation of adipogenesis may lead to an early consumption of the stem cell pool, and thus, may impair adipose tissue expandability postnatally, which may lead to differences in regional adipose tissue growth. We tested this hypothesis by analyzing global gene expression to identify expression patterns in subcutaneous abdominal, subcutaneous femoral, and omental adipose depots of baboon fetuses that have been altered by nutritional maternal deprivation. Adipose tissue was collected from baboon fetuses at 165 dG from mothers fed control or 30% nutrient-restricted diets (three females and one male in each group).
2011-12-16 | GSE34464 | GEO