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    Thermo Fisher genechip microarray data
    PLX3397 depletes microglia in organotypic tissue cultures. A , Entorhino-hippocampal tissue culture stained with DAPI nuclear stain. EC, entorhinal cortex; DG, dentate gyrus. Scale bar, 200 µm. B , C , Representative examples of tissue cultures stained for the microglial marker Iba1. Note homogeneous distribution of microglia in the control culture and depletion of microglia following PLX3397 treatment (50 n m , 18 d). Scale bars, 200 µm. D , Microglia cell counts in the respective groups (n control = 14 cultures, n PLX3397 = 15 cultures; Mann–Whitney test, U = 0). E-G , Affymetrix <t>Microarray</t> analysis of control cultures and cultures treated with PLX3397. E , Volcano plot represents fold changes and FDR p values of analyzed transcripts. Green represents significantly upregulated transcripts. Red represents significantly downregulated transcripts. F , Classification of differentially expressed transcripts; 97.5% of the differentially expressed transcripts are microglia-specific or microglia-related (for detailed results, see Extended Data ). G , Hierarchical clustering of differentially expressed gene sets characteristic of M0-, M1-, and M2-classified microglia. Each sample consisted of three pooled cultures ( n = 3 samples in each group). Colored dots represent individual data points. Data are mean ± SEM. *** p < 0.001.
    Genechip Microarray Data, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    genechip microarray data - by Bioz Stars, 2026-11
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    Images

    1) Product Images from "Microglial Cytokines Mediate Plasticity Induced by 10 Hz Repetitive Magnetic Stimulation"

    Article Title: Microglial Cytokines Mediate Plasticity Induced by 10 Hz Repetitive Magnetic Stimulation

    Journal: The Journal of Neuroscience

    doi: 10.1523/JNEUROSCI.2226-22.2023

    PLX3397 depletes microglia in organotypic tissue cultures. A , Entorhino-hippocampal tissue culture stained with DAPI nuclear stain. EC, entorhinal cortex; DG, dentate gyrus. Scale bar, 200 µm. B , C , Representative examples of tissue cultures stained for the microglial marker Iba1. Note homogeneous distribution of microglia in the control culture and depletion of microglia following PLX3397 treatment (50 n m , 18 d). Scale bars, 200 µm. D , Microglia cell counts in the respective groups (n control = 14 cultures, n PLX3397 = 15 cultures; Mann–Whitney test, U = 0). E-G , Affymetrix Microarray analysis of control cultures and cultures treated with PLX3397. E , Volcano plot represents fold changes and FDR p values of analyzed transcripts. Green represents significantly upregulated transcripts. Red represents significantly downregulated transcripts. F , Classification of differentially expressed transcripts; 97.5% of the differentially expressed transcripts are microglia-specific or microglia-related (for detailed results, see Extended Data ). G , Hierarchical clustering of differentially expressed gene sets characteristic of M0-, M1-, and M2-classified microglia. Each sample consisted of three pooled cultures ( n = 3 samples in each group). Colored dots represent individual data points. Data are mean ± SEM. *** p < 0.001.
    Figure Legend Snippet: PLX3397 depletes microglia in organotypic tissue cultures. A , Entorhino-hippocampal tissue culture stained with DAPI nuclear stain. EC, entorhinal cortex; DG, dentate gyrus. Scale bar, 200 µm. B , C , Representative examples of tissue cultures stained for the microglial marker Iba1. Note homogeneous distribution of microglia in the control culture and depletion of microglia following PLX3397 treatment (50 n m , 18 d). Scale bars, 200 µm. D , Microglia cell counts in the respective groups (n control = 14 cultures, n PLX3397 = 15 cultures; Mann–Whitney test, U = 0). E-G , Affymetrix Microarray analysis of control cultures and cultures treated with PLX3397. E , Volcano plot represents fold changes and FDR p values of analyzed transcripts. Green represents significantly upregulated transcripts. Red represents significantly downregulated transcripts. F , Classification of differentially expressed transcripts; 97.5% of the differentially expressed transcripts are microglia-specific or microglia-related (for detailed results, see Extended Data ). G , Hierarchical clustering of differentially expressed gene sets characteristic of M0-, M1-, and M2-classified microglia. Each sample consisted of three pooled cultures ( n = 3 samples in each group). Colored dots represent individual data points. Data are mean ± SEM. *** p < 0.001.

    Techniques Used: Staining, Marker, MANN-WHITNEY, Microarray

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    Microarray:

    Article Title: Interleukin-4 Receptor α Subunit Deficiency Alleviates Murine Intestinal Inflammation In Vivo Through the Enhancement of Intestinal Mucosal Barrier Function
    Article Snippet: .. Furthermore, the data were analyzed GeneChip microarray data using Transcriptome Analysis Console (TAC; Thermo Fisher Scientific, Waltham, MA, United States), GeneSpring (Silicon Genetics, Redwood City, CA, United States) and Ingenuity Pathway Analysis (IPA; Ingenuity Systems, Redwood City, CA, United States, http://www.ingenuity.com ) to extract significant genes, and identify the gene ontology and the canonical pathways associated with the differentially expressed genes. ..

    Article Title: An overview of Spotfire for gene-expression studies.
    Article Snippet: Spotfire DecisionSite (Spotfire, Inc.; http://www.spotfire.com) is a powerful data mining and visualization application with use in many disciplines.. Modules are available for use in various areas of research, e.g., support of gene expression analysis, proteomics, general statistical analysis, chemical lead discovery analysis, and geology.. Here the focus is on Spotfire’s utility in analyzing gene expression data obtained from DNA microarray experiments (Spotfire Decision Site for Functional Genomics).

    Article Title: Microglial Cytokines Mediate Plasticity Induced by 10 Hz Repetitive Magnetic Stimulation
    Article Snippet: .. Affymetrix GeneChip microarray data (CEL files) were analyzed using the Affymetrix Transcriptome Analysis Console (TAC version 4.0.2.15). ..

    Article Title: Young Leaf Chlorosis 2 encodes the stroma-localized heme oxygenase 2 which is required for normal tetrapyrrole biosynthesis in rice.
    Article Snippet: Main conclusion Rice heme oxygenase 2 (OsHO2) mutants are chlorophyll deficient with distinct tetrapyrrole metabolite and transcript profiles, suggesting a potential regulatory role of the stromal-localized OsHO2 in tetrapyrrole biosynthesis.. In plants, heme oxygenases (HOs) are classified into the subfamilies HO1 and HO2.. HO1 are highly conserved plastid enzymes required for synthesizing the chromophore in phytochromes which mediate a number of light-regulated responses.

    Article Title: Tissue and species distribution of the glutathione pathway transcriptome.
    Article Snippet: The goal of this study was to compare and contrast the basal gene expression levels of the various enzymes involved in glutathione metabolism among tissues and genders of the rat, mouse and canine.. The approach taken was to use Affymetrix GeneChip microarray data for rat, mouse and canine tissues, comparing intensity levels for individual probes between tissues and genders.. As was hypothesized, the relative expression in liver, lung, heart, kidney and testis varied from gene to gene, with differences of expression between tissues sometimes greater than a 1000-fold.

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    Article Snippet: doi:10.1111/ppl.12083 The Arabidopsis genome contains seven members of Hsp90.. Mutations in plastid AtHsp90.5 were reported to cause defects in chloroplast development and embryogenesis.. However, the exact function of plastid AtHsp90.5 has not yet been defined.

    Indirect Immunoperoxidase Assay:

    Article Title: Interleukin-4 Receptor α Subunit Deficiency Alleviates Murine Intestinal Inflammation In Vivo Through the Enhancement of Intestinal Mucosal Barrier Function
    Article Snippet: .. Furthermore, the data were analyzed GeneChip microarray data using Transcriptome Analysis Console (TAC; Thermo Fisher Scientific, Waltham, MA, United States), GeneSpring (Silicon Genetics, Redwood City, CA, United States) and Ingenuity Pathway Analysis (IPA; Ingenuity Systems, Redwood City, CA, United States, http://www.ingenuity.com ) to extract significant genes, and identify the gene ontology and the canonical pathways associated with the differentially expressed genes. ..

    Functional Assay:

    Article Title: An overview of Spotfire for gene-expression studies.
    Article Snippet: Spotfire DecisionSite (Spotfire, Inc.; http://www.spotfire.com) is a powerful data mining and visualization application with use in many disciplines.. Modules are available for use in various areas of research, e.g., support of gene expression analysis, proteomics, general statistical analysis, chemical lead discovery analysis, and geology.. Here the focus is on Spotfire’s utility in analyzing gene expression data obtained from DNA microarray experiments (Spotfire Decision Site for Functional Genomics).

    Gene Expression:

    Article Title: An overview of Spotfire for gene-expression studies.
    Article Snippet: Spotfire DecisionSite (Spotfire, Inc.; http://www.spotfire.com) is a powerful data mining and visualization application with use in many disciplines.. Modules are available for use in various areas of research, e.g., support of gene expression analysis, proteomics, general statistical analysis, chemical lead discovery analysis, and geology.. Here the focus is on Spotfire’s utility in analyzing gene expression data obtained from DNA microarray experiments (Spotfire Decision Site for Functional Genomics).

    Article Title: Young Leaf Chlorosis 2 encodes the stroma-localized heme oxygenase 2 which is required for normal tetrapyrrole biosynthesis in rice.
    Article Snippet: Main conclusion Rice heme oxygenase 2 (OsHO2) mutants are chlorophyll deficient with distinct tetrapyrrole metabolite and transcript profiles, suggesting a potential regulatory role of the stromal-localized OsHO2 in tetrapyrrole biosynthesis.. In plants, heme oxygenases (HOs) are classified into the subfamilies HO1 and HO2.. HO1 are highly conserved plastid enzymes required for synthesizing the chromophore in phytochromes which mediate a number of light-regulated responses.

    Produced:

    Article Title: An overview of Spotfire for gene-expression studies.
    Article Snippet: Spotfire DecisionSite (Spotfire, Inc.; http://www.spotfire.com) is a powerful data mining and visualization application with use in many disciplines.. Modules are available for use in various areas of research, e.g., support of gene expression analysis, proteomics, general statistical analysis, chemical lead discovery analysis, and geology.. Here the focus is on Spotfire’s utility in analyzing gene expression data obtained from DNA microarray experiments (Spotfire Decision Site for Functional Genomics).

    Software:

    Article Title: An overview of Spotfire for gene-expression studies.
    Article Snippet: Spotfire DecisionSite (Spotfire, Inc.; http://www.spotfire.com) is a powerful data mining and visualization application with use in many disciplines.. Modules are available for use in various areas of research, e.g., support of gene expression analysis, proteomics, general statistical analysis, chemical lead discovery analysis, and geology.. Here the focus is on Spotfire’s utility in analyzing gene expression data obtained from DNA microarray experiments (Spotfire Decision Site for Functional Genomics).

    Expressing:

    Article Title: Young Leaf Chlorosis 2 encodes the stroma-localized heme oxygenase 2 which is required for normal tetrapyrrole biosynthesis in rice.
    Article Snippet: Main conclusion Rice heme oxygenase 2 (OsHO2) mutants are chlorophyll deficient with distinct tetrapyrrole metabolite and transcript profiles, suggesting a potential regulatory role of the stromal-localized OsHO2 in tetrapyrrole biosynthesis.. In plants, heme oxygenases (HOs) are classified into the subfamilies HO1 and HO2.. HO1 are highly conserved plastid enzymes required for synthesizing the chromophore in phytochromes which mediate a number of light-regulated responses.

    other:

    Article Title: Fuzzy logic and related methods as a screening tool for detecting gene regulatory networks
    Article Snippet: 1566-2535/$ see front matter 2008 Elsevier B.V. A doi:10.1016/j.inffus.2008.11.008 * Corresponding author.. Tel.. : +1 502 852 3444; fax E-mail address: guy.brock@louisville.edu (G.N.



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    Image Search Results


    PLX3397 depletes microglia in organotypic tissue cultures. A , Entorhino-hippocampal tissue culture stained with DAPI nuclear stain. EC, entorhinal cortex; DG, dentate gyrus. Scale bar, 200 µm. B , C , Representative examples of tissue cultures stained for the microglial marker Iba1. Note homogeneous distribution of microglia in the control culture and depletion of microglia following PLX3397 treatment (50 n m , 18 d). Scale bars, 200 µm. D , Microglia cell counts in the respective groups (n control = 14 cultures, n PLX3397 = 15 cultures; Mann–Whitney test, U = 0). E-G , Affymetrix Microarray analysis of control cultures and cultures treated with PLX3397. E , Volcano plot represents fold changes and FDR p values of analyzed transcripts. Green represents significantly upregulated transcripts. Red represents significantly downregulated transcripts. F , Classification of differentially expressed transcripts; 97.5% of the differentially expressed transcripts are microglia-specific or microglia-related (for detailed results, see Extended Data ). G , Hierarchical clustering of differentially expressed gene sets characteristic of M0-, M1-, and M2-classified microglia. Each sample consisted of three pooled cultures ( n = 3 samples in each group). Colored dots represent individual data points. Data are mean ± SEM. *** p < 0.001.

    Journal: The Journal of Neuroscience

    Article Title: Microglial Cytokines Mediate Plasticity Induced by 10 Hz Repetitive Magnetic Stimulation

    doi: 10.1523/JNEUROSCI.2226-22.2023

    Figure Lengend Snippet: PLX3397 depletes microglia in organotypic tissue cultures. A , Entorhino-hippocampal tissue culture stained with DAPI nuclear stain. EC, entorhinal cortex; DG, dentate gyrus. Scale bar, 200 µm. B , C , Representative examples of tissue cultures stained for the microglial marker Iba1. Note homogeneous distribution of microglia in the control culture and depletion of microglia following PLX3397 treatment (50 n m , 18 d). Scale bars, 200 µm. D , Microglia cell counts in the respective groups (n control = 14 cultures, n PLX3397 = 15 cultures; Mann–Whitney test, U = 0). E-G , Affymetrix Microarray analysis of control cultures and cultures treated with PLX3397. E , Volcano plot represents fold changes and FDR p values of analyzed transcripts. Green represents significantly upregulated transcripts. Red represents significantly downregulated transcripts. F , Classification of differentially expressed transcripts; 97.5% of the differentially expressed transcripts are microglia-specific or microglia-related (for detailed results, see Extended Data ). G , Hierarchical clustering of differentially expressed gene sets characteristic of M0-, M1-, and M2-classified microglia. Each sample consisted of three pooled cultures ( n = 3 samples in each group). Colored dots represent individual data points. Data are mean ± SEM. *** p < 0.001.

    Article Snippet: Affymetrix GeneChip microarray data (CEL files) were analyzed using the Affymetrix Transcriptome Analysis Console (TAC version 4.0.2.15).

    Techniques: Staining, Marker, MANN-WHITNEY, Microarray

    Identification of miRNAs expressed in apoptotic cortical neurons and present in corresponding supernatant by miRNA microarray. ( a ) Representative images of cortical neurons isolated from C57BL/6 mice incubated with either 1 μM staurosporine or DMSO (0.1%) as solvent control for 8 h. Scale bar, 20 μm. Neurons and corresponding supernatant (S/N) were collected separately for small RNA enrichment and subsequent miRNA GeneChip analysis, as indicated by arrows. ( b ) Immunoblot depicting cleaved caspase-3 in C57BL/6 cortical neurons derived from 5 individual cell cultures after staurosporine (+) or DMSO (−) treatment. β-actin served as loading control. ( c ) Heat map of significantly differentially expressed miRNAs in apoptotic cortical neurons and corresponding S/N ( P < 0.01, Log2 Fold Change > 1) described above. Color scale corresponds to the robust multi-array average-processed miRNA expression values after averaging over replicates. Unstimulated neurons (control, n = 5), staurosporine-treated neurons ( n = 5), control S/N ( n = 5), apoptotic neuron S/N ( n = 4). miRNA IDs are depicted for significantly deregulated miRNAs in the S/N of apoptotic cortical neurons. ( d ) Volcano plots with significantly differentially expressed miRNA species indicated by black filling in apoptotic neurons and their conditioned S/N ( P < 0.01, Log2 Fold Change > 1)

    Journal: Molecular Neurodegeneration

    Article Title: MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration

    doi: 10.1186/s13024-021-00498-5

    Figure Lengend Snippet: Identification of miRNAs expressed in apoptotic cortical neurons and present in corresponding supernatant by miRNA microarray. ( a ) Representative images of cortical neurons isolated from C57BL/6 mice incubated with either 1 μM staurosporine or DMSO (0.1%) as solvent control for 8 h. Scale bar, 20 μm. Neurons and corresponding supernatant (S/N) were collected separately for small RNA enrichment and subsequent miRNA GeneChip analysis, as indicated by arrows. ( b ) Immunoblot depicting cleaved caspase-3 in C57BL/6 cortical neurons derived from 5 individual cell cultures after staurosporine (+) or DMSO (−) treatment. β-actin served as loading control. ( c ) Heat map of significantly differentially expressed miRNAs in apoptotic cortical neurons and corresponding S/N ( P < 0.01, Log2 Fold Change > 1) described above. Color scale corresponds to the robust multi-array average-processed miRNA expression values after averaging over replicates. Unstimulated neurons (control, n = 5), staurosporine-treated neurons ( n = 5), control S/N ( n = 5), apoptotic neuron S/N ( n = 4). miRNA IDs are depicted for significantly deregulated miRNAs in the S/N of apoptotic cortical neurons. ( d ) Volcano plots with significantly differentially expressed miRNA species indicated by black filling in apoptotic neurons and their conditioned S/N ( P < 0.01, Log2 Fold Change > 1)

    Article Snippet: Microarray data from the GeneChip miRNA 4.0 array (Thermo Fisher Scientific #902445, Waltham, MA, USA) were processed using the robust multi-array average (RMA) method on the R/Bioconductor platform [ ].

    Techniques: Microarray, Isolation, Incubation, Solvent, Control, Western Blot, Derivative Assay, Expressing

    (A) Entorhino-hippocampal tissue culture stained with DAPI nuclear stain (EC, entorhinal cortex; DG, dentate gyrus). Scale bar, 200 μm. (B, C) Representative examples of tissue cultures stained for the microglial marker Iba1. Note homogenous distribution of microglia in the control culture and almost complete depletion of microglia following PLX3397 treatment (50 nM, 18 days). Scale bars, 200 μm. (D) Microglia cell counts in the respective groups (n control = 14 cultures, n PLX(50nM) = 15 cultures; Mann-Whitney test, U = 0). (E-G) Affymetrix ® Microarray analysis of control cultures and cultures treated with PLX3397. (E) Volcano plot shows fold changes and FDR p-values of analyzed transcripts. Significantly upregulated transcripts are indicated in green, significantly downregulated transcripts are indicated in red. (F) Classification of differentially expressed transcripts. 97.5% of the differentially expressed transcripts are microglia-specific or microglia-related. (G) Hierarchical clustering of differentially expressed gene sets characteristic of M0-, M1-, and M2-classified microglia. Each sample consisted of 3 pooled cultures (n = 3 samples in each group). Individual data points are indicated by colored dots. Values represent mean ± s.e.m (***p < 0.001).

    Journal: bioRxiv

    Article Title: Microglia mediate synaptic plasticity induced by 10 Hz repetitive magnetic stimulation

    doi: 10.1101/2021.10.03.462905

    Figure Lengend Snippet: (A) Entorhino-hippocampal tissue culture stained with DAPI nuclear stain (EC, entorhinal cortex; DG, dentate gyrus). Scale bar, 200 μm. (B, C) Representative examples of tissue cultures stained for the microglial marker Iba1. Note homogenous distribution of microglia in the control culture and almost complete depletion of microglia following PLX3397 treatment (50 nM, 18 days). Scale bars, 200 μm. (D) Microglia cell counts in the respective groups (n control = 14 cultures, n PLX(50nM) = 15 cultures; Mann-Whitney test, U = 0). (E-G) Affymetrix ® Microarray analysis of control cultures and cultures treated with PLX3397. (E) Volcano plot shows fold changes and FDR p-values of analyzed transcripts. Significantly upregulated transcripts are indicated in green, significantly downregulated transcripts are indicated in red. (F) Classification of differentially expressed transcripts. 97.5% of the differentially expressed transcripts are microglia-specific or microglia-related. (G) Hierarchical clustering of differentially expressed gene sets characteristic of M0-, M1-, and M2-classified microglia. Each sample consisted of 3 pooled cultures (n = 3 samples in each group). Individual data points are indicated by colored dots. Values represent mean ± s.e.m (***p < 0.001).

    Article Snippet: We selected the winning model if the ΔBIC was at least 10 units less than for the null or previous model. Affymetrix GeneChip™ microarray data (CEL files) were analyzed using the Affymetrix Transcriptome Analysis Console (TAC version 4.0.2.15).

    Techniques: Staining, Marker, MANN-WHITNEY, Microarray