Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1125158 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29457719.fastq.gz | Fastqsanger.gz | |||
| SRR29457720.fastq.gz | Fastqsanger.gz | |||
| SRR29457721.fastq.gz | Fastqsanger.gz | |||
| SRR29457722.fastq.gz | Fastqsanger.gz | |||
| SRR29457723.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.
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Project description:We report a set of rapid, efficient and low-cost methods for ATAC-seq library construction and data analysis, realized large-scale and rapid sequencing. These methods can provide a reference for the study of epigenetic regulation of gene expression.
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Project description:For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation. However, these strategies can affect the match between the library and SWATH measurement, and thus larger library sizes do not necessarily correspond to improved SWATH quantification. Here, three fractionation strategies to increase local library size were compared to standard library building using replicate DDA injection: protein SDS-PAGE fractionation, peptide high-pH RP-HPLC fractionation and MS-acquisition gas phase fractionation. The impact of these libraries on SWATH performance was evaluated in terms of the number of extracted peptides and proteins, the match quality of the peptides and the extraction reproducibility of the transitions. These analyses were conducted using the hydrophilic proteome of differentiating human embryonic stem cells.
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