cdna microarray analysis illumina j.h  (Illumina Inc)

Journal: International Journal of Molecular Sciences

Article Title: A Dominant-Negative Mutant of ANXA7 Impairs Calcium Signaling and Enhances the Proliferation of Prostate Cancer Cells by Downregulating the IP3 Receptor and the PI3K/mTOR Pathway

doi: 10.3390/ijms24108818

Figure Lengend Snippet: ( A ) Comparative lipid-relevant gene expression profiles with the introduction of wt- ANXA7 and DN- ANXA7J in averaged PrCa array. cDNA microarray analysis was performed using Atlas Human Cancer 1.2 arrays and corresponding software AtlasImage 2.01 (Clontech, Palo Arto, CA, USA). Averaged wt- or mut- ANXA7 arrays for PrCa were created using prostate cell lines (LNCaP, DU145, and PC3). Wt/DN- ANXA7J ratio was assessed using the actual difference between the adjusted intensities after subtraction of the external background and the global normalization based on the sum method. Each of the presented genes was found on the outliers lists either in PrCa with the following criteria: R > 2 and difference threshold >4000. ( B ) Apoptotic rates including PS exposure with corresponding mTOR gene expression in response to wt/DN- ANXA7J or p53 in benign versus cancerous and prostate cells. Type I PCD rates as early apoptosis with PS exposure (grey columns) and late apoptosis with membrane permeabilization (black columns) by ANXAV-PE were compared with the vector in each category and presented as delta % (left scale). mTOR gene expression was compared with the averaged CELL array and presented as the actual difference between the adjusted intensities after subtraction of the external background and the global normalization based on the sum method (black line, right scale).

Article Snippet: The tumor-specific gene expression profiles in DU145 cells transfected with wt- ANXA7 , DN- ANXA7J , or p53 were determined using cDNA microarray analysis (Atlas Human Cancer 1.2 Arrays and AtlasImage 2.01 software, Clontech, Palo Alto, CA, USA).

Techniques: Expressing, Microarray, Software, Plasmid Preparation

Journal: Oncology Reports

Article Title: SPC25 promotes hepatocellular carcinoma metastasis via activating the FAK/PI3K/AKT signaling pathway through ITGB4

doi: 10.3892/or.2022.8302

Figure Lengend Snippet: SPC25 upregulates the expression of genes associated with ECM-receptor interactions and focal adhesion pathways. (A) The volcano map of DEGs (HCCLM3 silencing vs. control). (B) GO analysis showed that SPC25 exerts an influence on ECM-associated biological processes. (C) KEGG analysis, also revealing that SPC25 silencing exerts important effects on ECM-receptor interactions. (D) The genes associated with ECM-receptor interactions and focal adhesion were screened by microarray analysis, and subsequently confirmed by RT-qPCR (**P<0.01, independent-samples t-test, compared with the shNC group). SPC25, spindle pole body component 25 homolog; DEG, differentially expressed gene; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; ECM, extracellular matrix.

Article Snippet: The results of Agilent cDNA microarray analysis showed that SPC25 silencing was significantly correlated with ‘ECM receptor interactions’ which were mainly mediated by the interaction of laminin-332 and integrin α6β4 (ITGA6 and ITGB4).

Techniques: Expressing, Microarray, Quantitative RT-PCR

Journal: BMC Microbiology

Article Title: A comparison of two distinct murine macrophage gene expression profiles in response to Leishmania amazonensis infection

doi: 10.1186/1471-2180-12-22

Figure Lengend Snippet: Comparison of differentially expressed genes using microarray and RT-qPCR techniques . RT-qPCR was used to verify the differential expression of randomly selected genes (n = 27) by uninfected C57BL/6 and CBA macrophages (A), by L. amazonensis -infected C57BL/6 macrophages in comparison to uninfected cells (n = 7) (B), and by L. amazonensis -infected CBA macrophages in comparison to uninfected cells (n = 2) (C). Figure 1 (A-C) depicts only genes that were successfully verified using RT-qPCR. Resulting comparison values are expressed as mean values of log 2 ± SE from two independent experiments in comparison (A), and three independent experiments in comparisons (B) and (C), all performed in duplicate. The nonparametric Mann-Whitney test was used for comparison between uninfected cells, and Stouffer method was used to integrate the results from independent microarray and RT-qPCR analyses to determine significant differences between infected and uninfected cells (level of significance, p ≤ 0.05)

Article Snippet: Additionally, these authors found comparable fold-change values between the cDNA Affymetrix microarray analysis and the RTqPCR technique used for validation.

Techniques: Microarray, Quantitative RT-PCR, Expressing, Infection, MANN-WHITNEY

Journal: BMC Microbiology

Article Title: A comparison of two distinct murine macrophage gene expression profiles in response to Leishmania amazonensis infection

doi: 10.1186/1471-2180-12-22

Figure Lengend Snippet: Networks built using differentially expressed genes in uninfected macrophages from C57BL/6 and CBA mice . C57BL/6 and CBA macrophages were cultured separately and then processed for microarray analysis as described in Materials and Methods. The cell death and lipid metabolism network (A) and the cell-cell signaling and interaction network (B) were modeled using Ingenuity Pathway Analysis software v8.8 (IPA-Ingenuity Systems ® ). The above networks are displayed as a series of nodes (genes or gene products) and edges (or lines, corresponding to biological relationships between nodes). Nodes are displayed using shapes that represent the functional class of the gene product as indicated in the key. Nodes marked in green were found to be highly expressed in C57BL/6 macrophages in comparison to CBA. Nodes marked in red were found to be highly expressed in CBA macrophages compared to C57BL/6. The unmarked nodes were not identified in our samples; however, IPA ® added them to the networks due to their high probability of involvement in a given network. The node color intensity is an indication of the degree of up-(green) or down-(red) regulation of genes observed in the biological network analysis from uninfected C57BL/6 macrophages compared to CBA cells. Solid lines denote direct interactions, whereas dotted lines represent indirect interactions between the genes represented in this network.

Article Snippet: Additionally, these authors found comparable fold-change values between the cDNA Affymetrix microarray analysis and the RTqPCR technique used for validation.

Techniques: Cell Culture, Microarray, Software, Functional Assay

Journal: BMC Microbiology

Article Title: A comparison of two distinct murine macrophage gene expression profiles in response to Leishmania amazonensis infection

doi: 10.1186/1471-2180-12-22

Figure Lengend Snippet: Networks built using differentially expressed genes in L. amazonensis- infected and uninfected macrophages . C57BL/6 or CBA macrophages were cultured, infected and processed for microarray analysis as described in Materials and Methods. Considering the modulated genes in C57BL/6 infected macrophages, the immunological disease and cell morphology network (A), as well as the protein synthesis, cellular development and cell death network (B) were modeled by IPA ® . Considering the modulated genes in CBA infected macrophages, the lipid metabolism, cellular movement, and small molecule biochemistry network was built by IPA ® (C). C57BL/6 and CBA macrophages were cultured separately, then infected and processed for microarray analysis as described in Materials and Methods. Similar to Figure 2, the above networks are displayed as a series of nodes (genes or gene products) and edges (or lines, corresponding to biological relationships between nodes). Nodes are displayed using shapes as indicated in the key. Nodes marked in red were found to be highly expressed in infected macrophages. Nodes marked in green were found to be highly expressed in uninfected macrophages. Unmarked nodes were added by IPA ® due to a high degree of probability of involvement in a given network. The node color intensity is an indication of the degree of up-(red) or down-(green) regulation of genes observed in the biological network analysis from both C57BL/6 and CBA macrophages in response to infection. Solid lines denote direct interactions, whereas dotted lines represent indirect interactions between the genes represented in this network.

Article Snippet: Additionally, these authors found comparable fold-change values between the cDNA Affymetrix microarray analysis and the RTqPCR technique used for validation.

Techniques: Infection, Cell Culture, Microarray