ABSTRACT: Differential expression genes were normalized to fragments per kilobase of exon model per million mapped reads (RPKM) using EdgeR package in R with the criteria of fold change significantly greater than 1.5 and P<0.05. Gene ontology (GO) enrichment analysis of the DEGs was analyzed by using DAVID (the Database for Annotation, Visualization and Integrated Discovery, https://david.ncifcrf.gov). GO terms with corrected p <0.05 were considered significantly enriched. Gene Set Enrichment Analysis (GSEA) was performed to determine whether a defined set of genes shows statistically significant, consistent differences between Men1f/f and littermates Men1d/d decidual tissues.
Project description:Differential expression genes were normalized to fragments per kilobase of exon model per million mapped reads (RPKM) using EdgeR package in R with the criteria of fold change significantly greater than 2 or less than 0.5 and P<0.05.
Project description:A Toxoplasma gondii infection during pregnancy can result in spontaneous abortion, preterm labor, or congenital fetal defects. The decidual immune system plays a critical role in regulating the immune micro-environment and in the induction of immune tolerance. To better understand the factors that mediate the decidual immune response associated with the T. gondii infection, a large-scale study employing TMT proteomics was conducted to characterize the differential decidual immune proteomes from infected and uninfected human decidual immune cells samples. The decidual immune cells from 105 human voluntary abortion tissues were purified, and of the 5510 unique proteins identified, 181 proteins were found to be differentially abundant (>1.2-fold cutoff, P<0.05) in the T. gondii-infected decidual immune cells. 11 proteins of 181 differentially expressed proteins associated with trophoblast invasion, placental development, intrauterine fetal growth, and immune tolerance were verified using a quantitative real-time polymerase chain reaction and western blotting. This systematic research identified a broad range of immune factors in human decidual immune cells, shedding a new insight into the decidual immune molecular mechanism for abnormal pregnancy outcomes associated with T. gondii infection.
Project description:To detect the direct target genes of Menin and H3K4me3 in decidual stromal cells, decidual stromal cells are collected and subjected to ChIP-Seq. After aligned to mouse mm10 by STAR, peaks are called by MACS2. We found that Menin and H3K4me3 was significantly enriched at the transcription start site (TSS) of expressed genes (RPKM>1). A direct comparison of Menin and H3K4me3 ChIP-seq peaks at gene promoters showed a significantly strong positive correlation (R2=0.5888291). The promoters of 6,800 genes bound by Menin (92% of all genes with promoter bound by Menin) were also H3K4me3 modified.
Project description:This study evaluates the gene expression patterns in 36 decidual samples of women having gone through different types of child birth. The samples were profiled on Illumina Human HT-12_v4 BeadArrays. The analysis includes quality control and exploratory analysis of the dataset, followed by the identification of differentially expressed genes (DEGs) and finally, functional analysis for enrichment of KEGG pathways and GO terms amongst the DEGs. The statistical analysis was performed for six comparisons: Term labour (TL) vs Term not labour (TNL), TL vs Preterm labour (PTL), TL vs Preterm non-labour (PTNL), TNL vs PTL, TNL vs PTNL and PTL vs PTNL. This study evaluates the gene expression levels from decidual samples obtained from women giving birth with different types of labour. The dataset was composed of 36 Illumina Human HT-12_v4 expression BeadArrays.
Project description:To identify the differentially expressed genes in normal gastric mucosa and gastric cancer tissues, we employed the microarray profiling analysis. Genes with greater than 2-fold change and P-value <0.05 were identified as differentially expressed genes. From this dataset, we obtained differentially expressed genes by cluster analysis and enriched GOs was identified by Gene set enrichment analysis (GSEA) analysis, microtubule GO was one of the most enriched GOs, and the gene KIF14 was selected to go on to the next step in the study.
Project description:To investigate gene expression changes induced by Lysophosphatidic acid receptor 3 (LPA3) activation in peri-implantation uteri, we performed microarray analysis in LPA3 agonist (T13)-injected pseudopregnant uteri. On 3.5 dpc, pseudopregnant mice were subjected with intrautero-injection of vehicle (0.01% BSA-PBS) or T13 and then uteri were dissected 24-36 hr after the injection. We found that several thousand genes were up- or down-regulated by T13 injection. Interestingly, well-known decidual markers such as Bmp2 and Wnt4 were dramatically induced by T13, which we certificated in quantitive RT-PCR.
Project description:Purpose: Taurine promotes the activation of plasmacytoid dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation. Methods: Mouse plasmacytoid dendritic cells were stimulated with R837, together with or without taurine for 12 hours. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/). Results: Genes in the TLR7-IRF7 pathway were augmented by taurine. As a result, the production of type I IFNs increased upon taurine treatment.
Project description:Our objective was to identify genes differentially expressed between control and Ezh2 cKO decidua, and to compare this set of genes with a previously identified gene set of H3K27me3-marked decidual genes that are putatively silenced by EZH2/PRC2 (Nancy et al. JCI. 2018). RNA was isolated from whole tissue decidua and myometrium of control and Ezh2 cKO mice. Sequencing provided was 731 million total reads with an average of 84.5% of these reads aligning uniquely to the mouse genome. Reads uniquely mapped to known mRNAs were used to identify gene expression changes between housing conditions using DESeq2. We found that 2530 protein-coding genes were differentially expressed within the decidua and 521 were differentially expressed in the myometrium (FDR<0.05, excluding genes whose normalized read counts were less than 30 averaged across samples). Hypergeometric analysis revealed a strong enrichment for previously identified H3K27me3 targets within genes overexpressed in Ezh2 cKO decidua.
Project description:Purpose: NCF1 gene single nucleotide polymorphism (SNP) rs201802880 (G to A change) promotes the activation of plasmacytoid dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation. Methods: Mouse plasmacytoid dendritic cells isolated from GG, AG or AA allele mice, were stimulated with R848 for 12 hours. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/). Results: Genes in the TLR7-IRF7 pathway were augmented by NCF1 SNP. As a result, the production of type I IFNs increased in AA pDCs.