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Conjoint analysis of RNA-seq and Solexa sequencing data of bovine mammary epithelial cells isolated from Chinese Holstein cows with high and low milk fat percentages

ABSTRACT: For RNA-seq, the sequencing library of each RNA sample was prepared by using Ion Total RNA-Seq Kit v2. For Solexa suquencing, we download the data obtained by a previous study in our laboratory. Genes and miRNAs were considered differentially expressed according to log2FC >1 or log2FC <-1and FDR <0.05. All target genes regulated by DERs were predicted by the combination of miRbase (http://www.mirbase.org) and TargetScan (http://www.targetscan.org). All the predicted target genes were intersected with the DEGs obtained by RNA-seq, and then the DEGs and DERs were obtained by a combined analysis.In total, 190 DEGs were regulated by 33 DERs that were significantly enriched in 488 GO terms and 12 KEGG pathways (p <0.05).This is of great significance for research on miRNAs and functional genes for the milk fat percentage- and marker-assisted selection of dairy cattle.

ORGANISM(S): Bos taurus

PROVIDER: GSE137488 | GEO | 2019/09/25

REPOSITORIES: GEO

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Project description:Radiation-induced pulmonary fibrosis (RIPF) is the most common bottleneck of radiation therapy (RT) that limits its tumor-killing effect. Up to date, there is no effective therapeutic agent for RIPF treatment due to absence of realistic preclinical models. Lungs of mice exposed to focal, highly localized dose of 75Gy-100Gy represents short time-taking (up to 6 weeks) modality for mimicking recent advanced RT, stereotactic body RT-associated lung fibrosis. However, extensive fibrosis and possibility of animal lethality resulted from exposure to high dose raises a question regarding the appropriate dose threshold for limiting unnecessary responses and obtain clinically relevant results. We observed in preliminary trials that lung tissues of 65Gy-exposed mice are still able to develop inflammation and fibrosis at the same time cap. But the molecular changes associated with dose reduction is still unknown. To examine this, bulk RNA from 65Gy and 75Gy irradiated as well as normal lung tissues of mice were obtained, and analysed using computational approach to uncover the transcriptomal similarities and differences between the differentially irradiated samples. Differentially expressed genes (DEGs) were analysed and 2-week and 6-week intersected DEGs as well as 65 and 75Gy exclusive DEGs at 2-week and 6-week time points were detected using venn diagramme. Expression direction of intersected DEGs between 65Gy and 75Gy was checked and found to be consistent at both inflammation and fibrosis stages proven visually by MDS and heatmap graphs. All-times intersected DEGs are 488 and involved in inflammation, cytokine production, and cell proliferation; 2-week intersected DEGs are 221 and involved in cell cycle and DNA damage; 6-week intersected DEGs are 403 and involved in immunoglobin production, extracellular matrix (ECM) deposition, and ECM-receptor interactions. Interestingly, only 75Gy exclusive DEGs of 2 and 6 weeks presented inflammation and fibrosis-related biological process, respectively. These include anti-inflammatory process, cytokine production, EMT, vasculogenesis, and angiogenesis. These results suggested that 65Gy maybe a better dose for delivering less exaggerated, clinically relevant inflammation and fibrotic events, and thus, it can be utilised in establishing appropriate preclinical models for studying RIPF pathology and therapy.

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Conjoint analysis of RNA-seq and Solexa sequencing data of bovine mammary epithelial cells isolated from Chinese Holstein cows with high and low milk fat percentages

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