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Identification of AIA_H related genes and BHGZD therapeutic effect related genes. [RNA-Seq]

ABSTRACT: To obtain AIA_H related genes [the significant differentially expressed genes (DEGs) of AIA_H model group vs. Normal control group] and BHGZD therapeutic effect related genes [DEGs of BHGZD treatment group vs. AIA_H model group], the microarray analysis was carried out.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE190522 | GEO | 2021/12/11

REPOSITORIES: GEO

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Project description:Abstract Background: Cerebral ischemia-reperfusion (I/R) frequently caused the late-onset neuronal damage. Breviscapine has a promote in autophagy of microvascular endothelial cells in I/R and it can inhibit the oxidative damage and apoptosis. However, the mediation mechanism of breviscapine on neuronal cell death is unclear. Methods: Firstly, transcriptome sequencing was performed on three groups of mice neuronal normal group (Control group), oxygen-glucose deprivation/reoxygenation group (OGD/R group) and breviscapine administration group (Therapy group). Differentially expressed genes (DEGs) between OGD/R and Control groups, and between Therapy and OGD/R groups were obtained by limma package. The N6-methyladenosine (m6A) methylation related DEGs were selected out by the Pearson correlation analysis. Then, prediction and confirmation of drug targets were performed by Swiss Target Prediction and UniProt Knowledgebase (UniProtKB) datebase, and key genes were obtained by Pearson correlation analysis between m6A-related DEGs and drug target genes. Next, gene set enrichment (GSEA) analysis and Ingenuity pathway analysis (IPA) were used to obtain the pathways of key genes. Finally, a circRNA-miRNA-mRNA network was constructed based on the mRNAs, circRNAs and miRNAs. Results: 2250 DEGs between OGD/R and Control groups and 757 DEGs between Therapy and OGD/R groups were selected out by differential analysis. A total of 7 m6A related DEGs including Arl4d, Gm10653, Gm1113, Kcns3, Olfml2a, Stk26 and Tfcp2l1 were obtained by Pearson correlation analysis. Four key genes (Tfcp2l1, Kcns3, Olfml2a and Arl4d) were acquired, and GSEA showed that these key genes were significantly participated in DNA repair, e2f targets and g2m checkpoint. IPA revealed that Tfcp2l1 played a significant role in human embryonic stem cell pluripotency. The circRNA-miRNA-mRNA network showed that the mmu_circ_0001258 regulated the Tfcp2l1 by mmu-miR-301b-3p. Conclusions: In conclusion, four key genes including Tfcp2l1, Kcns3, Olfml2a and Arl4d significantly associated with the treatment of OGD/R by breviscapine were acquired, which would provide a theoretical basis for clinical trials.

Project description:Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) is an important cucurbit crop grown worldwide. Watermelon fruit quality, fertility, and the seed setting rate are closely related to male flower development. In this study, the different developmental stages of flower buds of the watermelon variety Xinteda Zhengkang 9 were distinguished by cytological observation, and transcriptome sequencing analysis was performed subsequently. Acetocarmine staining of anthers was performed and the longitudinal and transverse diameters of the unopened male flower buds were measured. Cytological observations of anthers at different developmental stages showed that the anther grew from the tetrad to the mature stage, and the longitudinal and transverse diameters of the flower buds increased. The length of the male flower buds also changed significantly during development. Transcriptome sequencing analysis at four periods, the tetrad (A group), mononuclear (B group), dikaryophase (C group), and mature stages (D group). Total 16288 differentially expressed genes (DEGs) were detected in the four stages, with the prolongation of developmental stages the number of DEGs increased gradually in the comparison groups, such as there was 2014, 3259, 4628, 1490, 3495 and 1132 DEGs were revealed in six comparison groups (A-VS-B, A-VS-C, A-VS-D, B-VS-C, B-VS-D, and C-VS-D), respectively. Gene ontology (GO) and KEGG enrichment analysis showed that the DEGs were mainly enriched in cellular component and starch and sucrose metabolism, phenylpropanoid biosynthesis and pentose sugar, etc. Finally, we totally screened 59 DEGs were in the six comparison groups, and most of them were up-regulated, interestingly, we find one pollen-specific protein (Cla001608) was significantly up-regulated (the value of log2Fold Change up to 17.32), which indicating that it may play important role in the development of male flowers. This work provides insight into the molecular basis of the developmental stages of male flowers in watermelon and may aid in dominant cross breeding.

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Identification of AIA_H related genes and BHGZD therapeutic effect related genes. [RNA-Seq]

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