Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA645822

PRJNA645822: Transcriptomic profiling of cerebrum, liver, and muscle tissues of 50 days fetuses in response to early maternal nutrient restriction (cattle)

Source: NCBI / GSE154299
Submission Date: Jul 13 2020
Release Date: Feb 08 2021
Update Date: Feb 08 2021

Summary: 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.

Overall Design: 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.

GEN Datasets:
GEND000161
Strategy:
Species:
Tissue:
Development Stage:
Protocol
Growth Protocol: 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).
Treatment Protocol: 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).
Extract Protocol: 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).
Library Construction Protocol: 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.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
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]