previous affymetrix genechip dna microarray data  (Thermo Fisher)

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

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

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