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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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    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: Copy number variation as a tool for implementing pregnancy as an aging model
    Article Snippet: Whole-genome profiling of CNVs in the centenarians’ and control blood samples was carried out using Affymetrix microarray-based CNV calling. .. Total DNA was extracted from 287 elderly and 230 controls and then hybridized to Affymetrix microarray GeneChip, which consists of 21,560 distinct CNV regions. ..

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    Article Snippet: .. The Affymetrix GeneChip Microarray analyses were performed on the same RNA twice and the values were averaged. ..

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    Article Snippet: .. Transcriptome profiling was performed using the Affymetrix GeneChip microarray system. ..

    Article Title: Systems and methods for high throughput compound library creation
    Article Snippet: For instance, by way of a non-limiting example, in some embodiments, the microarrays such as the Affymetrix GeneChip microarray, a high density oligonucleotide gene expression array, is used. .. Each gene on an Affymetrix microarray GeneChip is typically represented by a probe set consisting of 11 different pairs of 25-bp oligos covering features of the transcribed region of that gene. ..

    other:

    Article Title: Artificial intelligence-based determination of analyte data for base calling
    Article Snippet: Further examples of commercially available microarrays that can be used include, for example, an Affymetrix® GeneChip® microarray or other microarray synthesized in accordance with techniques sometimes referred to as VLSIPS™ (Very Large Scale Immobilized Polymer Synthesis) technologies.

    Article Title: Intensity extraction from oligonucleotide clusters for base calling
    Article Snippet: Further examples of commercially available microarrays that can be used include, for example, an Affymetrix® GeneChip® microarray or other microarray synthesized in accordance with techniques sometimes referred to as VLSIPS™ (Very Large Scale Immobilized Polymer Synthesis) technologies.

    Article Title: Method and system for fluorescence lifetime based sequencing
    Article Snippet: Further examples of commercially available microarrays and techniques for their manufacture include, for example, an Affymetrix® GeneChip® microarray or other microarray synthesized in accordance with techniques sometimes referred to as VLSIPS™ (Very Large Scale Immobilized Polymer Synthesis) technologies as described, for example, in U.S. Pat.

    Article Title: Training data generation for artificial intelligence-based sequencing
    Article Snippet: Further examples of commercially available microarrays that can be used include, for example, an Affymetrix® GeneChip® microarray or other microarray synthesized in accordance with techniques sometimes referred to as VLSIPS™ (Very Large Scale Immobilized Polymer Synthesis) technologies.



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    Identification of miRNAs expressed in apoptotic cortical neurons and present in corresponding supernatant by miRNA <t>microarray.</t> ( 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)
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    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.
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    Image Search Results


    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

    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

    (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