PRJNA645822: Transcriptomic profiling of cerebrum, liver, and muscle tissues of 50 days fetuses in response to early maternal nutrient restriction (cattle)
概要: 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.
项目整体设计: Angus-cross heifers (n = 14) with average initial body weight = 313 ± 24.9 kg were randomly assigned at breeding to receive dietary intake of either 100% of NRC energy requirements for 0.45 kg/day of body weight gain (control; CON, n = 7) or were fed a diet to delivery 60% of CON intake (restricted; RES, n = 7). On day 50 of gestation, cerebrum (n = 14), liver (n = 14), and muscle (n = 14) were collected from fetuses following ovariohysterectomy.
| 生长方案: |
Heifers were acclimated to individual bunk feeding (American Calan, Northwood, NH) for 2 wk before the beginning of the trial. All heifers were exposed to the 5-d CO-Synch + CIDR estrus synchronization protocol and bred via AI to a common sire at 12 h after observed estrus. Immediately post-breeding, heifers were randomly assigned to one of two treatment groups. The diet was delivered via total mixed ration and consisted of grass hay, corn silage, alfalfa haylage, as well as a grain and mineral mix. Dried distillers grains with solubles (53.4% NDF, 31.3% CP) were supplemented in addition to the TMR and fed to achieve the target nutrient content of the CON and RES diets (Crouse et al., 2019). |
| 处理方案: |
Control heifers (CON, n = 7) received 100% of (NRC, 2000) requirements for 0.45 kg/d gain to reach 80% of mature body weight at first calving. Restricted heifers (RES, n = 7) were placed on a 40% global nutrient restriction, which was accomplished by reducing total diet delivery to 60% of the control delivery (Crouse et al., 2019). |
| 提取方案: |
RNA was extracted with the RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) and quantified using a NanoDrop for 260/280 (Min = 1.93, Max = 2.10) and 260/230 (Min = 1.53, Max = 2.23) ratios as well as Quant-iT RiboGreen Assay Kit for RNA concentration (Min = 280.3 ng/µL, Max = 2680 ng/µL; Invitrogen, Carlsbas, CA). RNA integrity was measured with the Agilent TapeStation/BioAnalyzer (Agilent Technologies, Santa Clara, CA) for RNA quality (Min = 5.7, Max = 9.5). |
| 建库方案: |
RNA-seq library creations were strand specific. RNA sequencing analysis was conducted on the Illumina HiSeq 2500 platform and multiplexed with 21 samples per lane (42 samples total: 14 liver, 14 muscle, and 14 cerebrum) using 50-bp paired-end reads at a depth of 2 × 10.4M reads/sample in both forward and reverse directions. |
| 分子类型: |
poly(A)+ RNA |
| 库的片段类型: |
PAIRED |
| 库的链类型: |
Forward |
| 测序平台: |
ILLUMINA |
| 测序仪型号: |
Illumina HiSeq 2500 |
| 链特异性: |
Specific |
| 数据来源 |
GEN样本编号 |
GEN数据集编号 |
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项目编号 |
样本编号 |
样本名称 |
生物样本编号 |
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最后更新时间 |
物种 |
种族 |
族裔 |
年龄 |
年龄单位 |
性别 |
来源名称 |
组织 |
细胞类型 |
细胞亚型 |
细胞系 |
疾病 |
疾病状态 |
发育阶段 |
突变/变异 |
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Condition Detail |
生长方案 |
处理方案 |
提取方案 |
建库方案 |
分子类型 |
库的片段类型 |
链特异性 |
库的链类型 |
加标（Spike-In） |
测序方法 |
测序平台 |
测序仪型号 |
细胞数 |
测序片段数 |
碱基数 |
平均测序片段长度_1 |
平均测序片段长度_2 |
唯一比对率 |
多重比对率 |
覆盖度 |
Cerebrum, liver, and muscle regulatory networks uncover maternal nutrition effects in developmental programming of beef cattle during early pregnancy.
Scientific reports . 2021-02-02 [PMID:
33531552]
