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cdna microarray analysis illumina j.h  (Illumina Inc)


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    Structured Review

    Illumina Inc cdna microarray analysis illumina j.h
    Cdna Microarray Analysis Illumina J.H, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cdna+microarray+analysis/illumina+cdna+microarray/pm33741394-167-7-7
    Average 90 stars, based on 1 article reviews
    cdna microarray analysis illumina j.h - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    other:

    Article Title: Age-specific transcriptional response to stroke.
    Article Snippet: Increased age is a major risk factor for stroke incidence and post-ischemic mortality.. To develop ageadjusted therapeutic interventions, a clear understanding of the complexity of age-related postischemic mechanisms is essential.. Transient occlusion of the middle cerebral arteryda model that closely resembles human strokedwas used to induce cerebral infarction in mice of 4 different ages (2, 9, 15, 24 months).

    Generated:

    Article Title: Loss of ANCO1 repression at AIB1/YAP targets drives breast cancer progression
    Article Snippet: .. Heatmaps were generated by heatmap function in R. Illumina cDNA array RNA was extracted from cell lines in duplicate using RNeasy Mini Kit (Qiagen, Hilden, Germany), and quality was assessed by Bioanalyzer. ..

    Microarray:

    Article Title: Biological Significance of HORM-A Domain Containing Protein 1 (HORMAD1) in Epithelial Ovarian Carcinoma
    Article Snippet: .. cDNA microarray was performed using the Illumina platform on the 2774 ovarian cancer cells that were treated in 10 cm cell-culture plates with either HOMRAD1 (8.0μg) or control siRNA (8.0 μg) in triplicate using RNAiFect transfection reagent (Qiagen; Valencia, CA) per manufacturer’s recommendations. ..


    Article Title: cDNA Microarray Gene Expression Profiling of Hedgehog Signaling Pathway Inhibition in Human Colon Cancer Cells
    Article Snippet: .. HT29 and GC3/c1 cells were subsequently treated with GANT61 (20 μM) for 24 hr, RNA was extracted, and changes in gene expression were determined by Illumina cDNA microarray profiling. ..

    Article Title: Folliculin Interacting Protein-1 Maintains Metabolic Homeostasis During B Cell Development by Modulating AMPK, mTORC1, and TFE3
    Article Snippet: .. These results collectively suggest that in B cell progenitors, Fnip1 is required for retention of TFE3 in the cytosol under nutrient replete conditions, when mTORC1 is activated. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIGURE 5. caption a7 Fnip1 regulates TFE3 nuclear localization in B cell progenitors. ( A ) Median similarity (a measure of image overlap, lower panel) of TFE3 IC staining and nuclear staining (DAPI), and representative images (upper panels) of B220 + IgM − cells in Fnip1 +/− or Fnip1 −/− BM as measured by imaging flow cytometry. p<0.0001 one-way ANOVA. ( B ) Expression of selected TFE3 target genes as measured using Illumina cDNA microarray of FACs-sorted B220 + IgM − pro- and pre-B cells, Fnip1 −/− vs. WT, n=3 mice/group. ( C ) Schematic model of signaling inside Fnip1 -deficient B cells compared to normal B cells under nutrient replete or AA restricted conditions, showing dysregulation of mTORC1 and TFE3 localization in the absence of Fnip1. ..

    Control:

    Article Title: Biological Significance of HORM-A Domain Containing Protein 1 (HORMAD1) in Epithelial Ovarian Carcinoma
    Article Snippet: .. cDNA microarray was performed using the Illumina platform on the 2774 ovarian cancer cells that were treated in 10 cm cell-culture plates with either HOMRAD1 (8.0μg) or control siRNA (8.0 μg) in triplicate using RNAiFect transfection reagent (Qiagen; Valencia, CA) per manufacturer’s recommendations. ..

    Transfection:

    Article Title: Biological Significance of HORM-A Domain Containing Protein 1 (HORMAD1) in Epithelial Ovarian Carcinoma
    Article Snippet: .. cDNA microarray was performed using the Illumina platform on the 2774 ovarian cancer cells that were treated in 10 cm cell-culture plates with either HOMRAD1 (8.0μg) or control siRNA (8.0 μg) in triplicate using RNAiFect transfection reagent (Qiagen; Valencia, CA) per manufacturer’s recommendations. ..

    Knockdown:

    Article Title: A synthetic Toll-like receptor 3 ligand mitigates profibrotic fibroblast responses by inducing autocrine interferon signaling
    Article Snippet: .. Pretreatment of the fibroblasts with the endosomal TLR inhibitors chloroquine or bafilomycin ( and data not shown), RNAi-mediated knockdown of endogenous TLR3 , and peptide blockade of TRIF to inactivate TLR3 signaling (data not shown), each failed to abrogate the down-regulation of Col1A1 or ASMA elicited in fibroblasts by Poly I:C. In contrast, TLR3 inhibitors effectively blocked Poly I:C-induced stimulation of IL-6, as expected (data not shown). fig ft0 fig mode=article f1 Figure 3 caption a4 caption a8 Poly I:C inhibition of fibrotic gene expression is TLR3-independent To characterize the changes elicited by Poly I:C treatment of fibroblasts at the genome-wide scale, total RNA was isolated from foreskin fibroblasts incubated for 24 h with or without Poly I:C and hybridized to Illumina cDNA microarrays containing 44,000 probes. ..

    Inhibition:

    Article Title: A synthetic Toll-like receptor 3 ligand mitigates profibrotic fibroblast responses by inducing autocrine interferon signaling
    Article Snippet: .. Pretreatment of the fibroblasts with the endosomal TLR inhibitors chloroquine or bafilomycin ( and data not shown), RNAi-mediated knockdown of endogenous TLR3 , and peptide blockade of TRIF to inactivate TLR3 signaling (data not shown), each failed to abrogate the down-regulation of Col1A1 or ASMA elicited in fibroblasts by Poly I:C. In contrast, TLR3 inhibitors effectively blocked Poly I:C-induced stimulation of IL-6, as expected (data not shown). fig ft0 fig mode=article f1 Figure 3 caption a4 caption a8 Poly I:C inhibition of fibrotic gene expression is TLR3-independent To characterize the changes elicited by Poly I:C treatment of fibroblasts at the genome-wide scale, total RNA was isolated from foreskin fibroblasts incubated for 24 h with or without Poly I:C and hybridized to Illumina cDNA microarrays containing 44,000 probes. ..

    Gene Expression:

    Article Title: A synthetic Toll-like receptor 3 ligand mitigates profibrotic fibroblast responses by inducing autocrine interferon signaling
    Article Snippet: .. Pretreatment of the fibroblasts with the endosomal TLR inhibitors chloroquine or bafilomycin ( and data not shown), RNAi-mediated knockdown of endogenous TLR3 , and peptide blockade of TRIF to inactivate TLR3 signaling (data not shown), each failed to abrogate the down-regulation of Col1A1 or ASMA elicited in fibroblasts by Poly I:C. In contrast, TLR3 inhibitors effectively blocked Poly I:C-induced stimulation of IL-6, as expected (data not shown). fig ft0 fig mode=article f1 Figure 3 caption a4 caption a8 Poly I:C inhibition of fibrotic gene expression is TLR3-independent To characterize the changes elicited by Poly I:C treatment of fibroblasts at the genome-wide scale, total RNA was isolated from foreskin fibroblasts incubated for 24 h with or without Poly I:C and hybridized to Illumina cDNA microarrays containing 44,000 probes. ..

    Article Title: cDNA Microarray Gene Expression Profiling of Hedgehog Signaling Pathway Inhibition in Human Colon Cancer Cells
    Article Snippet: .. HT29 and GC3/c1 cells were subsequently treated with GANT61 (20 μM) for 24 hr, RNA was extracted, and changes in gene expression were determined by Illumina cDNA microarray profiling. ..

    Genome Wide:

    Article Title: A synthetic Toll-like receptor 3 ligand mitigates profibrotic fibroblast responses by inducing autocrine interferon signaling
    Article Snippet: .. Pretreatment of the fibroblasts with the endosomal TLR inhibitors chloroquine or bafilomycin ( and data not shown), RNAi-mediated knockdown of endogenous TLR3 , and peptide blockade of TRIF to inactivate TLR3 signaling (data not shown), each failed to abrogate the down-regulation of Col1A1 or ASMA elicited in fibroblasts by Poly I:C. In contrast, TLR3 inhibitors effectively blocked Poly I:C-induced stimulation of IL-6, as expected (data not shown). fig ft0 fig mode=article f1 Figure 3 caption a4 caption a8 Poly I:C inhibition of fibrotic gene expression is TLR3-independent To characterize the changes elicited by Poly I:C treatment of fibroblasts at the genome-wide scale, total RNA was isolated from foreskin fibroblasts incubated for 24 h with or without Poly I:C and hybridized to Illumina cDNA microarrays containing 44,000 probes. ..

    Isolation:

    Article Title: A synthetic Toll-like receptor 3 ligand mitigates profibrotic fibroblast responses by inducing autocrine interferon signaling
    Article Snippet: .. Pretreatment of the fibroblasts with the endosomal TLR inhibitors chloroquine or bafilomycin ( and data not shown), RNAi-mediated knockdown of endogenous TLR3 , and peptide blockade of TRIF to inactivate TLR3 signaling (data not shown), each failed to abrogate the down-regulation of Col1A1 or ASMA elicited in fibroblasts by Poly I:C. In contrast, TLR3 inhibitors effectively blocked Poly I:C-induced stimulation of IL-6, as expected (data not shown). fig ft0 fig mode=article f1 Figure 3 caption a4 caption a8 Poly I:C inhibition of fibrotic gene expression is TLR3-independent To characterize the changes elicited by Poly I:C treatment of fibroblasts at the genome-wide scale, total RNA was isolated from foreskin fibroblasts incubated for 24 h with or without Poly I:C and hybridized to Illumina cDNA microarrays containing 44,000 probes. ..

    Incubation:

    Article Title: A synthetic Toll-like receptor 3 ligand mitigates profibrotic fibroblast responses by inducing autocrine interferon signaling
    Article Snippet: .. Pretreatment of the fibroblasts with the endosomal TLR inhibitors chloroquine or bafilomycin ( and data not shown), RNAi-mediated knockdown of endogenous TLR3 , and peptide blockade of TRIF to inactivate TLR3 signaling (data not shown), each failed to abrogate the down-regulation of Col1A1 or ASMA elicited in fibroblasts by Poly I:C. In contrast, TLR3 inhibitors effectively blocked Poly I:C-induced stimulation of IL-6, as expected (data not shown). fig ft0 fig mode=article f1 Figure 3 caption a4 caption a8 Poly I:C inhibition of fibrotic gene expression is TLR3-independent To characterize the changes elicited by Poly I:C treatment of fibroblasts at the genome-wide scale, total RNA was isolated from foreskin fibroblasts incubated for 24 h with or without Poly I:C and hybridized to Illumina cDNA microarrays containing 44,000 probes. ..

    Staining:

    Article Title: Folliculin Interacting Protein-1 Maintains Metabolic Homeostasis During B Cell Development by Modulating AMPK, mTORC1, and TFE3
    Article Snippet: .. These results collectively suggest that in B cell progenitors, Fnip1 is required for retention of TFE3 in the cytosol under nutrient replete conditions, when mTORC1 is activated. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIGURE 5. caption a7 Fnip1 regulates TFE3 nuclear localization in B cell progenitors. ( A ) Median similarity (a measure of image overlap, lower panel) of TFE3 IC staining and nuclear staining (DAPI), and representative images (upper panels) of B220 + IgM − cells in Fnip1 +/− or Fnip1 −/− BM as measured by imaging flow cytometry. p<0.0001 one-way ANOVA. ( B ) Expression of selected TFE3 target genes as measured using Illumina cDNA microarray of FACs-sorted B220 + IgM − pro- and pre-B cells, Fnip1 −/− vs. WT, n=3 mice/group. ( C ) Schematic model of signaling inside Fnip1 -deficient B cells compared to normal B cells under nutrient replete or AA restricted conditions, showing dysregulation of mTORC1 and TFE3 localization in the absence of Fnip1. ..

    Imaging:

    Article Title: Folliculin Interacting Protein-1 Maintains Metabolic Homeostasis During B Cell Development by Modulating AMPK, mTORC1, and TFE3
    Article Snippet: .. These results collectively suggest that in B cell progenitors, Fnip1 is required for retention of TFE3 in the cytosol under nutrient replete conditions, when mTORC1 is activated. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIGURE 5. caption a7 Fnip1 regulates TFE3 nuclear localization in B cell progenitors. ( A ) Median similarity (a measure of image overlap, lower panel) of TFE3 IC staining and nuclear staining (DAPI), and representative images (upper panels) of B220 + IgM − cells in Fnip1 +/− or Fnip1 −/− BM as measured by imaging flow cytometry. p<0.0001 one-way ANOVA. ( B ) Expression of selected TFE3 target genes as measured using Illumina cDNA microarray of FACs-sorted B220 + IgM − pro- and pre-B cells, Fnip1 −/− vs. WT, n=3 mice/group. ( C ) Schematic model of signaling inside Fnip1 -deficient B cells compared to normal B cells under nutrient replete or AA restricted conditions, showing dysregulation of mTORC1 and TFE3 localization in the absence of Fnip1. ..

    Flow Cytometry:

    Article Title: Folliculin Interacting Protein-1 Maintains Metabolic Homeostasis During B Cell Development by Modulating AMPK, mTORC1, and TFE3
    Article Snippet: .. These results collectively suggest that in B cell progenitors, Fnip1 is required for retention of TFE3 in the cytosol under nutrient replete conditions, when mTORC1 is activated. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIGURE 5. caption a7 Fnip1 regulates TFE3 nuclear localization in B cell progenitors. ( A ) Median similarity (a measure of image overlap, lower panel) of TFE3 IC staining and nuclear staining (DAPI), and representative images (upper panels) of B220 + IgM − cells in Fnip1 +/− or Fnip1 −/− BM as measured by imaging flow cytometry. p<0.0001 one-way ANOVA. ( B ) Expression of selected TFE3 target genes as measured using Illumina cDNA microarray of FACs-sorted B220 + IgM − pro- and pre-B cells, Fnip1 −/− vs. WT, n=3 mice/group. ( C ) Schematic model of signaling inside Fnip1 -deficient B cells compared to normal B cells under nutrient replete or AA restricted conditions, showing dysregulation of mTORC1 and TFE3 localization in the absence of Fnip1. ..

    Expressing:

    Article Title: Folliculin Interacting Protein-1 Maintains Metabolic Homeostasis During B Cell Development by Modulating AMPK, mTORC1, and TFE3
    Article Snippet: .. These results collectively suggest that in B cell progenitors, Fnip1 is required for retention of TFE3 in the cytosol under nutrient replete conditions, when mTORC1 is activated. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIGURE 5. caption a7 Fnip1 regulates TFE3 nuclear localization in B cell progenitors. ( A ) Median similarity (a measure of image overlap, lower panel) of TFE3 IC staining and nuclear staining (DAPI), and representative images (upper panels) of B220 + IgM − cells in Fnip1 +/− or Fnip1 −/− BM as measured by imaging flow cytometry. p<0.0001 one-way ANOVA. ( B ) Expression of selected TFE3 target genes as measured using Illumina cDNA microarray of FACs-sorted B220 + IgM − pro- and pre-B cells, Fnip1 −/− vs. WT, n=3 mice/group. ( C ) Schematic model of signaling inside Fnip1 -deficient B cells compared to normal B cells under nutrient replete or AA restricted conditions, showing dysregulation of mTORC1 and TFE3 localization in the absence of Fnip1. ..



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    Image Search Results


    ( 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).

    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

    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.

    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

    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)

    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

    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.

    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

    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.

    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