Next Generation Sequencing Facilitates Quantitative Analysis of CRC cells with low DUOX2 expression compared with the control group
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ABSTRACT: Purpose: The purpose of this study was to analyze changes in the cell genome along with the downregulation of DUOX2, as well as changes in gene enrichment pathways, so as to find the downstream target genes of DUOX2 Conclusions: Our study is the first detailed analysis of DUOX2's effect on the genome of CRC cells.We concluded that changes in DUOX2 gene levels can lead to activation of multiple tumor-related signaling pathways, and that NGS provides a more comprehensive and accurate method for quantitative and qualitative assessment of cell mRNA content.
Project description:Purpose: The purpose of this study was to analyze changes in the cell genome along with the downregulation of SLCO1B3, as well as changes in gene enrichment pathways, so as to find the downstream target genes of SLCO1B3 Conclusions: Our study is the first detailed analysis of SLCO1B3's effect on the genome of CRC cells.We concluded that changes in SLCO1B3 gene levels can lead to activation of multiple tumor-related signaling pathways, and that NGS provides a more comprehensive and accurate method for quantitative and qualitative assessment of cell mRNA content.
Project description:Next Generation Sequencing Facilitates Quantitative Analysis of CRC cells with low DUOX2 expression compared with the control group
Project description:To evaluate the roles of DUOX2 in flagellin- induced inflammatory response in mouse nasal mucosa. Wild type (Duox2+/+) and Duox2 knockout (Duox2-/-) mice were stimulated with 1 M-NM-<g/ml of flagellin for 4h. 422 genes (> 2 fold) were up-regulated in nasal mucosa of Duox2+/+ that was treated with flagellin and the full list of genes is presented in Supplemental Table II. These genes included the following defense- and immune response-related genes : Cytokine/chemokine-related genes (CCL20, CCR2, CCR5, CXCL2, CXCL5, CXCL9, CXCL16, IL18RAP, TNFAIP2, IL1B EAR2, FPR1), Granulocyte-related genes (IL8RB, MPO, PRG2, PPBP, PRG3), interferon-related genes (IFITM6, IFI47), macrophage related genes (IL1B, S100A9), and T-cell mediated immune response related genes (H2-Q6, IL1F9). In addition, signal transduction (PPBP, OLFR60, P2RY10) and cell adhesion (SELL, SELP, ICAM1, DSG1A, DSG3, VCAM1) related genes were also increased by flagellin treatment. These genes were selected based on the biological processes and molecular functions of their gene ontology. However, the increase of inflammation and immune response related genes by flagellin treatment were diminished in the nasal mucosa of the Duox2-/- mice compared with that of Duox2+/+ mice. Wild type (Duox2+/+) and Duox2 knockout (Duox2-/-) mice received either PBS (control) or flagellin (5 ug/ml) intranasally for 4h.
Project description:To evaluate the roles of DUOX2 in flagellin- induced inflammatory response in mouse nasal mucosa. Wild type (Duox2+/+) and Duox2 knockout (Duox2-/-) mice were stimulated with 1 μg/ml of flagellin for 4h. 422 genes (> 2 fold) were up-regulated in nasal mucosa of Duox2+/+ that was treated with flagellin and the full list of genes is presented in Supplemental Table II. These genes included the following defense- and immune response-related genes : Cytokine/chemokine-related genes (CCL20, CCR2, CCR5, CXCL2, CXCL5, CXCL9, CXCL16, IL18RAP, TNFAIP2, IL1B EAR2, FPR1), Granulocyte-related genes (IL8RB, MPO, PRG2, PPBP, PRG3), interferon-related genes (IFITM6, IFI47), macrophage related genes (IL1B, S100A9), and T-cell mediated immune response related genes (H2-Q6, IL1F9). In addition, signal transduction (PPBP, OLFR60, P2RY10) and cell adhesion (SELL, SELP, ICAM1, DSG1A, DSG3, VCAM1) related genes were also increased by flagellin treatment. These genes were selected based on the biological processes and molecular functions of their gene ontology. However, the increase of inflammation and immune response related genes by flagellin treatment were diminished in the nasal mucosa of the Duox2-/- mice compared with that of Duox2+/+ mice.
Project description:The purpose of the study is to compare the protein changes between cirrhosis control and therapy groups for bone marrow-sorted LSK cells.
Project description:We sequenced mRNA transcripts from three isogenic M3 serotype GAS strains, parental (MGAS10870), complement (10870::rocAM1), and deletion (10870ΔrocA). There were no significant changes between the parental and revertant strain. Comparison of the parental and complemented strain revealed several virulence factors were up-regulated in the parental strain where RocA function was diminished. We concluded that RocA, through direct or indirect mechanisms, is able to control numerous virulence genes and this lack of RocA regulation increases expression of virulence factors, which contributes to the hyper-virulent state of serotype M3 GAS.
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analyze genes of different expression in gastric cancer cells between arv-825 treatment group and control group and to evaluate protocols for optimal high-throughput data analysis
Project description:Purpose of study was to investigate whole genome expression changes of a strain with deletion of the two-component system TctD-TctE and determine genes dysregulate relative to the parental wildtype to gain insight into possible regulatory targets of TctD-TctE. TctD-TctE is a two-component system in Pseudomonas aeruginosa that responds to and regulates uptake of tricarboxylic acids such as citric acid. It accomplishes this through derepression of the porin encoding the gene opdH, thereby regulating influx of citrate metabolites from the surrounding environment. Deletion of the tctED operon (ΔtctED) resulted in a reduced growth phenotype when citric acid is present in media. In the ΔtctED strain the presence of citric acid was found to have an inhibitory effect on growth. When the alternative carbon source arginine was present, wildtype levels of growth could not be restored. Static cultures of ΔtctED had low cell density in the presence of citric acid but maintained the same levels of biofilm formation compared to conditions when no citric acid was present. This suggests a dysregulation of biofilm formation in the presence of citric acid. In the ΔtctED strain there was also greater accumulation of tobramycin within the biofilm compared to the PA14 wildtype strain. Additionally, analysis of whole-genome expression found that multiple metabolic genes were dysregulated in ΔtctED. Here it is concluded that TctD-TctE is involved in biofilm tolerance to tobramycin in the presence of citrate metabolites.
Project description:We sequenced mRNA transcripts from three isogenic M3 serotype GAS strains, parental (MGAS10870), complement (10870::rocAM1), and deletion (10870?rocA). There were no significant changes between the parental and revertant strain. Comparison of the parental and complemented strain revealed several virulence factors were up-regulated in the parental strain where RocA function was diminished. We concluded that RocA, through direct or indirect mechanisms, is able to control numerous virulence genes and this lack of RocA regulation increases expression of virulence factors, which contributes to the hyper-virulent state of serotype M3 GAS. GAS strains were grown to mid-exponential phase, total RNA isolated, rRNA depleted, cDNA libraries synthesized, and libraries analyzed using Illumina MiSeq and CLC Genomics Workbench version 7.5.1 RNA-seq software.