Supplementary MaterialsAdditional file 1: Table S1. S8. Weighted gene co-expression correlation
Supplementary MaterialsAdditional file 1: Table S1. S8. Weighted gene co-expression correlation network analysis (WGCNA) of differential manifestation genes. a Differentially indicated genes after irradiation (2?h vs. 0?h, 8?h vs. 0?h, 8?h vs. PGE1 enzyme inhibitor 2?h) in the P6 or P10 BMSCs were extracted to apply WGCNA analysis. b Warmth map showing the co-expression modules by WGCNA. c Dendrogram from gene co-expression network analysis of samples from 0?h to 8?h time points. Modules of co-expressed genes were assigned colour. Correlations between gene co-expression modules. Module plots the top 15 hub genes and the top 50 connections along with the GO term enrichment of module MEturquoise (d), MEblack (e) and MEblue (f). The blue collection represents negative correlation. The red collection represents positive correlation. The size of point represents the number of genes associated with additional genes. (TIF 2238 kb) 13287_2019_1191_MOESM14_ESM.tif (2.1M) GUID:?5CAC9628-B124-4B4A-8EF7-8B709DC19125 Additional file 15: Table S7. KEGG pathway enrichment for co-expression modules from WGCNA analysis. (XLSX 108 kb) 13287_2019_1191_MOESM15_ESM.xlsx (117K) GUID:?697369E4-DF16-4AD8-834D-D670C0C3068F Data Availability StatementAll data generated or analyzed during this study have been included in this published article and its supplementary information documents. The datasets assisting the results of this article are available in NCBIs gene Manifestation Omnibus and are accessible through GEO Series accession quantity GSExxxxxx. Abstract Background Bone marrow stromal cells (BMSCs) are extensively used in regeneration therapy and cytology experiments simulate how BMSCs respond to radiation. Due to the small number and the heterogeneity of main isolated BMSCs, considerable in vitro development is usually required before software, which affects the cellular characteristics and gene manifestation of BMSCs. However, whether the radiation response of BMSCs changes during in vitro development is unclear. Methods In this study, BMSCs were passaged in vitro and irradiated PGE1 enzyme inhibitor at passage 6 (P6) and passage 10 (P10). Then, apoptosis, the cell cycle, senescence, the cytokine secretion and the gene manifestation profile were analysed for the P6, P10, and non-irradiated (control) BMSCs at different post-irradiation time points. Results The P6 BMSCs experienced a lower percentage of apoptotic cells than the P10 BMSCs at 24 and 48?h post-irradiation but not compared to that of the settings at 2 and 8?h post-irradiation. The P6 BMSCs experienced a lower percentage of cells in S phase and a higher percentage in G1 phase than the P10 BMSCs at 2 and 8?h post-irradiation. The radiation had similar Mouse monoclonal to IGF2BP3 effects within the senescent cell level and impaired immunomodulation capacity of the P6 and P10 BMSCs. Regardless of whether they were irradiated, the P6 and P10 BMSCs constantly indicated a distinctive set of genes. The upregulated genes were enriched in pathways including the cell cycle, DNA replication and oocyte meiosis. Then, a subset of conserved irradiation response genes across the BMSCs was recognized, comprising 12 differentially upregulated genes and 5 differentially downregulated genes. These genes were especially associated PGE1 enzyme inhibitor with the p53 signaling pathway, DNA damage and DNA restoration. Furthermore, validation experiments revealed the mRNA and protein levels of these conserved genes were different between the P6 and P10 BMSCs after irradiation. Weighted gene co-expression network analysis supported these findings and further exposed the effects of cell passage within the irradiation response in BMSCs. Summary The results indicated that cell passage in vitro affected the irradiation response of BMSCs via molecular mechanisms that mediated variations in apoptosis, the cell cycle, senescence and the cytokine secretion. Therefore, accurate cell passage information isn’t just important for transplantation therapy but also for long term studies on the radiation response in BMSCs. Electronic supplementary material The online version of this article (10.1186/s13287-019-1191-3) contains supplementary material, which is available to authorized users. test was performed to compare P6 and P10 BMSCs with significance arranged at a value of less than 0.05. *value and false finding rate (FDR).