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genechip r dna microarrays  (Thermo Fisher)


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    Thermo Fisher genechip r dna microarrays
    Genechip R Dna Microarrays, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/genechip+microarray+data/DNA/pmc02660910-19-10-9
    Average 99 stars, based on 1 article reviews
    genechip r dna microarrays - by Bioz Stars, 2026-09
    99/100 stars

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    Related Articles

    DNA Extraction:

    Article Title: A national study confirms a low occurrence of antimicrobial resistance amongst Escherichia coli isolates from the caecae of Australian meat chickens
    Article Snippet: .. DNA was extracted using the MagMAXTM Multi-Sample DNA Extraction Kit (Thermo Fisher Scientific, USA), following the manufacturer’s instructions. .. DNA libraries were prepared using the Celero chemistry (Tecan) with a modified reaction volume deviating from the manufacturer’s standard protocol.

    Concentration Assay:

    Article Title: Development of a high-resolution multiplex qPCR method to profile microbial consortia in spaceflight water recovery systems
    Article Snippet: 3 mL of broth culture from each strain was harvested by centrifugation and the genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen), following the manufacturer's protocol for cultured cells. .. DNA concentration and purity were assessed using a NanoDrop spectrophotometer. ..

    Article Title: Integrated genomic, transcriptomic, and metabolomic profile analysis reveals molecular mechanism underlying meat quality traits in Chinese Kangle chickens
    Article Snippet: .. We extracted genomic DNA from blood samples using the phenol/chloroform method and quantified DNA concentration/quality using a Nanodrop-2000 spectrophotometer (Thermo Fisher Scientific, MA, USA). .. In total, 273 Chinese Kangle chickens were genotyped for 52,180 SNPs using the “Jingxin NO.1” 55 K Beadchip by following the manufacturer's protocol (Chinese Academy of Agricultural Sciences, Beijing, China) ( ).

    Spectrophotometry:

    Article Title: Development of a high-resolution multiplex qPCR method to profile microbial consortia in spaceflight water recovery systems
    Article Snippet: 3 mL of broth culture from each strain was harvested by centrifugation and the genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen), following the manufacturer's protocol for cultured cells. .. DNA concentration and purity were assessed using a NanoDrop spectrophotometer. ..

    Article Title: Integrated genomic, transcriptomic, and metabolomic profile analysis reveals molecular mechanism underlying meat quality traits in Chinese Kangle chickens
    Article Snippet: .. We extracted genomic DNA from blood samples using the phenol/chloroform method and quantified DNA concentration/quality using a Nanodrop-2000 spectrophotometer (Thermo Fisher Scientific, MA, USA). .. In total, 273 Chinese Kangle chickens were genotyped for 52,180 SNPs using the “Jingxin NO.1” 55 K Beadchip by following the manufacturer's protocol (Chinese Academy of Agricultural Sciences, Beijing, China) ( ).

    Polymerase Chain Reaction:

    Article Title: Combinatorial engineering of enzyme and pathway for efficient β-farnesene bioproduction in Yarrowia lipolytica
    Article Snippet: The codon-optimized exogenous AaFS gene and its mutant variants synthesized by GenScript (Nanjing, China) were tailored for Y. lipolytica expression. .. PCR amplification was performed using primers listed in (Phusion® High-Fidelity DNA Polymerase, Thermo Fisher Scientific). ..

    Amplification:

    Article Title: Combinatorial engineering of enzyme and pathway for efficient β-farnesene bioproduction in Yarrowia lipolytica
    Article Snippet: The codon-optimized exogenous AaFS gene and its mutant variants synthesized by GenScript (Nanjing, China) were tailored for Y. lipolytica expression. .. PCR amplification was performed using primers listed in (Phusion® High-Fidelity DNA Polymerase, Thermo Fisher Scientific). ..

    Viscosity:

    Article Title: Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer
    Article Snippet: .. Qubit quantification indicated acceptable DNA concentrations; however, NanoDrop measurements showed low 260/230 ratios (e.g., 0.3–1.2), and the DNA exhibited a brown coloration and increased viscosity. ..

    other:

    Article Title: Integrative genomic analysis and gene expression patterns reveal a cardio-neuroendocrine signaling network for heat adaptation in geographically diverse chickens
    Article Snippet: DNA extraction was performed, checked for DNA quality using 1% agarose gel electrophoresis and NanoDrop 2000 (A260/280 ratio), and finally libraries were sequenced on the DNBSEQ-T7 platform.

    Modification:

    Article Title: Amino acid starvation and iron limitation facilitate the biofilm formation of Klebsiella pneumoniae within urine
    Article Snippet: .. All enzymes required for restriction digestion and DNA modification were sourced from Thermo Fisher Scientific (Waltham, MA, USA) and handled in accordance with the supplier's protocols. ..

    Purification:

    Article Title: Identification of biofilm-associated genes in Arcobacter butzleri
    Article Snippet: For that, the DNA of the P8 strain was extracted using Lysing Matrix E tubes (MP Biomedicals, France) and a Bead Mill 4 Mini Homogenizer (Fisher Scientific, USA). .. After purification with AMPure XP beads (Beckman Coulter, USA), DNA quantification was performed by a Qubit fluorometer (Invitrogen, USA) using the Qubit 1X dsDNA HS assay kit (Invitrogen, USA). .. DNA libraries were then prepared using the Rapid Sequencing Kit V14 (Oxford Nanopore Technologies, UK) and loaded into a Flonge flow cell (Oxford Nanopore Technologies, UK) for sequencing.



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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