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Agilent technologies microchip device
Microchip Device, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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microchip device - by Bioz Stars, 2020-05
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Sequencing:

Article Title: Impact of Amorphous SiO2 Nanoparticles on a Living Organism: Morphological, Behavioral, and Molecular Biology Implications
Article Snippet: .. RNA-seq analysis Prior to sequencing, RNA amount and quality were quantified by capillary electrophoresis on a microchip device (BioAnalyzer 2100, Agilent). ..

Electrophoresis:

Article Title: Impact of Amorphous SiO2 Nanoparticles on a Living Organism: Morphological, Behavioral, and Molecular Biology Implications
Article Snippet: .. RNA-seq analysis Prior to sequencing, RNA amount and quality were quantified by capillary electrophoresis on a microchip device (BioAnalyzer 2100, Agilent). ..

MicroChIP Assay:

Article Title: Impact of Amorphous SiO2 Nanoparticles on a Living Organism: Morphological, Behavioral, and Molecular Biology Implications
Article Snippet: .. RNA-seq analysis Prior to sequencing, RNA amount and quality were quantified by capillary electrophoresis on a microchip device (BioAnalyzer 2100, Agilent). ..

RNA Sequencing Assay:

Article Title: Impact of Amorphous SiO2 Nanoparticles on a Living Organism: Morphological, Behavioral, and Molecular Biology Implications
Article Snippet: .. RNA-seq analysis Prior to sequencing, RNA amount and quality were quantified by capillary electrophoresis on a microchip device (BioAnalyzer 2100, Agilent). ..

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  • 88
    Agilent technologies data analysis microarray
    Chronic Ctr infection of hFT organoids is characterized by early activation of inflammatory and paracrine signaling responses. a Representative confocal images of organoids infected with CtrD at 3, 24, and 80 d p.i., showing continuing presence of bacterial inclusions (red) within epithelial host cells (green). Scale bar: 20 µm. The WB of protein lysates from chronic infection at 2 months p.i. from three independent donors shows the presence of actively replicating bacteria (HSP60 protein). b Whole-mount 3D composite images of acute Ctr infection at 34 and 96 h p.i. showing a change in the localization of the bacteria ( Ctr , red) from the inclusions within the primarily infected host cells (left panel) to the lumen of the organoid (right panel) (β-catenin, green). Scale bar: 50 µm. c Still images as a time course from Supplementary Movie 1 demonstrate stepwise extrusion of bacterial inclusions to the lumen. Scale bar: 60 µm. d Different genital Ctr serovars D, K, and E establish chronic infection in the organoids and maintain growth at 1 month p.i., as shown in the WB of the protein lysates harvested at acute and chronic phase. e Venn diagram showing extensive overlap between three different donors in the genes differentially expressed in response to Ctr infection, as detected by <t>microarray</t> analysis at 72 h p.i., with 976 genes regulated in all samples. f Ingenuity pathway analysis, suggesting strong activation of pro-inflammatory signaling, in particular interferon-β, which was independently confirmed by WB and detection of phospho STAT1 in infected samples with interferon-β treated organoids as positive control. g Table of activated paracrine pathways in the acute Ctr infection based on ingenuity upstream regulator analysis IPA. h GSEA analysis of fallopian tube (FT) organoid stem cell signature genes 13 compared to differential gene expression in infected vs. non-infected organoids at 3 d p.i. shows significant enrichment (ES = 0.44, p
    Data Analysis Microarray, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/data analysis microarray/product/Agilent technologies
    Average 88 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    data analysis microarray - by Bioz Stars, 2020-05
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    99
    Agilent technologies microarray analysis
    The mRNA expression of NFAT1 and Fas obtained from <t>microarray</t> analysis in 111 clinical samples was analyzed by cluster analysis and Pearson correlation analysis. (A) NFAT1 was overexpressed in high-grade gliomas. (A, B) The expression of NFAT1 significantly correlated with the expression of Fas in gliomas. (C) Western bot showed that NFAT1 was highly expressed in GBM clinical samples as well as in U87 and U251 cells, compared with low-grade glioma and normal brain tissue samples. The graph is a representative of three independent experiments.
    Microarray Analysis, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 1221 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/microarray analysis/product/Agilent technologies
    Average 99 stars, based on 1221 article reviews
    Price from $9.99 to $1999.99
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    93
    Agilent technologies whole human genome microarray analysis
    Validation of potential prognostic markers by Taqman ® assay-based real-time PCR . 85 marker genes including the minimal set of 54 genes identified to best distinguish the luminal A and the basal-like subtypes were validated by TaqMan ® Gene Expression assays. Profile correlation analysis showed the expression profile across the 20 tumor samples determined by the three <t>microarray</t> platforms and by TaqMan ® Gene Expression assays are highly correlated with median correlation coefficient R > 0.9 and a rate of good correlation (R > 0.8) of 81–88%.
    Whole Human Genome Microarray Analysis, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/whole human genome microarray analysis/product/Agilent technologies
    Average 93 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    whole human genome microarray analysis - by Bioz Stars, 2020-05
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    Chronic Ctr infection of hFT organoids is characterized by early activation of inflammatory and paracrine signaling responses. a Representative confocal images of organoids infected with CtrD at 3, 24, and 80 d p.i., showing continuing presence of bacterial inclusions (red) within epithelial host cells (green). Scale bar: 20 µm. The WB of protein lysates from chronic infection at 2 months p.i. from three independent donors shows the presence of actively replicating bacteria (HSP60 protein). b Whole-mount 3D composite images of acute Ctr infection at 34 and 96 h p.i. showing a change in the localization of the bacteria ( Ctr , red) from the inclusions within the primarily infected host cells (left panel) to the lumen of the organoid (right panel) (β-catenin, green). Scale bar: 50 µm. c Still images as a time course from Supplementary Movie 1 demonstrate stepwise extrusion of bacterial inclusions to the lumen. Scale bar: 60 µm. d Different genital Ctr serovars D, K, and E establish chronic infection in the organoids and maintain growth at 1 month p.i., as shown in the WB of the protein lysates harvested at acute and chronic phase. e Venn diagram showing extensive overlap between three different donors in the genes differentially expressed in response to Ctr infection, as detected by microarray analysis at 72 h p.i., with 976 genes regulated in all samples. f Ingenuity pathway analysis, suggesting strong activation of pro-inflammatory signaling, in particular interferon-β, which was independently confirmed by WB and detection of phospho STAT1 in infected samples with interferon-β treated organoids as positive control. g Table of activated paracrine pathways in the acute Ctr infection based on ingenuity upstream regulator analysis IPA. h GSEA analysis of fallopian tube (FT) organoid stem cell signature genes 13 compared to differential gene expression in infected vs. non-infected organoids at 3 d p.i. shows significant enrichment (ES = 0.44, p

    Journal: Nature Communications

    Article Title: Chronic Chlamydia infection in human organoids increases stemness and promotes age-dependent CpG methylation

    doi: 10.1038/s41467-019-09144-7

    Figure Lengend Snippet: Chronic Ctr infection of hFT organoids is characterized by early activation of inflammatory and paracrine signaling responses. a Representative confocal images of organoids infected with CtrD at 3, 24, and 80 d p.i., showing continuing presence of bacterial inclusions (red) within epithelial host cells (green). Scale bar: 20 µm. The WB of protein lysates from chronic infection at 2 months p.i. from three independent donors shows the presence of actively replicating bacteria (HSP60 protein). b Whole-mount 3D composite images of acute Ctr infection at 34 and 96 h p.i. showing a change in the localization of the bacteria ( Ctr , red) from the inclusions within the primarily infected host cells (left panel) to the lumen of the organoid (right panel) (β-catenin, green). Scale bar: 50 µm. c Still images as a time course from Supplementary Movie 1 demonstrate stepwise extrusion of bacterial inclusions to the lumen. Scale bar: 60 µm. d Different genital Ctr serovars D, K, and E establish chronic infection in the organoids and maintain growth at 1 month p.i., as shown in the WB of the protein lysates harvested at acute and chronic phase. e Venn diagram showing extensive overlap between three different donors in the genes differentially expressed in response to Ctr infection, as detected by microarray analysis at 72 h p.i., with 976 genes regulated in all samples. f Ingenuity pathway analysis, suggesting strong activation of pro-inflammatory signaling, in particular interferon-β, which was independently confirmed by WB and detection of phospho STAT1 in infected samples with interferon-β treated organoids as positive control. g Table of activated paracrine pathways in the acute Ctr infection based on ingenuity upstream regulator analysis IPA. h GSEA analysis of fallopian tube (FT) organoid stem cell signature genes 13 compared to differential gene expression in infected vs. non-infected organoids at 3 d p.i. shows significant enrichment (ES = 0.44, p

    Article Snippet: Microarray expression profiling and data analysis Microarray experiments were performed as dual-color or single-color hybridizations on either 4 × 44 K human catalogue (Agilent-026652) or 8 × 60 K human custom (Agilent-048908) microarrays comprising identical features for coding genes.

    Techniques: Infection, Activation Assay, Western Blot, Microarray, Positive Control, Indirect Immunoperoxidase Assay, Expressing

    The mRNA expression of NFAT1 and Fas obtained from microarray analysis in 111 clinical samples was analyzed by cluster analysis and Pearson correlation analysis. (A) NFAT1 was overexpressed in high-grade gliomas. (A, B) The expression of NFAT1 significantly correlated with the expression of Fas in gliomas. (C) Western bot showed that NFAT1 was highly expressed in GBM clinical samples as well as in U87 and U251 cells, compared with low-grade glioma and normal brain tissue samples. The graph is a representative of three independent experiments.

    Journal: PLoS ONE

    Article Title: PMA and Ionomycin Induce Glioblastoma Cell Death: Activation-Induced Cell-Death-Like Phenomena Occur in Glioma Cells

    doi: 10.1371/journal.pone.0076717

    Figure Lengend Snippet: The mRNA expression of NFAT1 and Fas obtained from microarray analysis in 111 clinical samples was analyzed by cluster analysis and Pearson correlation analysis. (A) NFAT1 was overexpressed in high-grade gliomas. (A, B) The expression of NFAT1 significantly correlated with the expression of Fas in gliomas. (C) Western bot showed that NFAT1 was highly expressed in GBM clinical samples as well as in U87 and U251 cells, compared with low-grade glioma and normal brain tissue samples. The graph is a representative of three independent experiments.

    Article Snippet: The mRNA expression of NFAT1and Fas obtained from microarray analysis in 111 clinical samples was analyzed with cluster analysis and Pearson correlation analysis.

    Techniques: Expressing, Microarray, Western Blot

    The genomic map of total lncRNAs and deregulated LncRNAs in chromosomes of mouse. The distribution of LncRNAs in chromosomes of mouse is marked in blue. The upregulated LncRNAs are highlighed in red and the downregulated lncRNAs are highlighted in green. The length of the bars represents the folds of LncRNAs expression change. Microarray assays revealed the existence of a total of 20073 LncRNAs in mouse livers. The numbers and symbols represent chromosome numbers.

    Journal: PLoS ONE

    Article Title: Silencing of Long Noncoding RNA AK139328 Attenuates Ischemia/Reperfusion Injury in Mouse Livers

    doi: 10.1371/journal.pone.0080817

    Figure Lengend Snippet: The genomic map of total lncRNAs and deregulated LncRNAs in chromosomes of mouse. The distribution of LncRNAs in chromosomes of mouse is marked in blue. The upregulated LncRNAs are highlighed in red and the downregulated lncRNAs are highlighted in green. The length of the bars represents the folds of LncRNAs expression change. Microarray assays revealed the existence of a total of 20073 LncRNAs in mouse livers. The numbers and symbols represent chromosome numbers.

    Article Snippet: Overall, real time PCR assays validated the accuracy of LncRNA profile determined by microarray analysis.

    Techniques: Expressing, Microarray

    Validation of potential prognostic markers by Taqman ® assay-based real-time PCR . 85 marker genes including the minimal set of 54 genes identified to best distinguish the luminal A and the basal-like subtypes were validated by TaqMan ® Gene Expression assays. Profile correlation analysis showed the expression profile across the 20 tumor samples determined by the three microarray platforms and by TaqMan ® Gene Expression assays are highly correlated with median correlation coefficient R > 0.9 and a rate of good correlation (R > 0.8) of 81–88%.

    Journal: BMC Genomics

    Article Title: Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms

    doi: 10.1186/1471-2164-7-127

    Figure Lengend Snippet: Validation of potential prognostic markers by Taqman ® assay-based real-time PCR . 85 marker genes including the minimal set of 54 genes identified to best distinguish the luminal A and the basal-like subtypes were validated by TaqMan ® Gene Expression assays. Profile correlation analysis showed the expression profile across the 20 tumor samples determined by the three microarray platforms and by TaqMan ® Gene Expression assays are highly correlated with median correlation coefficient R > 0.9 and a rate of good correlation (R > 0.8) of 81–88%.

    Article Snippet: Agilent whole human genome microarray analysis The Agilent Whole Human Genome Oligo Microarray contains 44,000 60-mer oligonucleotide probes representing 41,000 unique genes and transcripts [ ].

    Techniques: TaqMan Assay, Real-time Polymerase Chain Reaction, Marker, Expressing, Microarray

    Validation of the luminal A and basal-like subtypes using three microarray platforms . (A) Unsupervised hierarchical clustering of 20 breast tumor tissues analyzed by Applied Biosystems (two replicates per sample), Stanford cDNA and Agilent arrays using the 510 mapped intrinsic genes. The data from each platform were first transformed independently and then combined for clustering: the level of expression of each gene in each sample (Applied Biosystems microarrays: normalized signal intensity; Stanford cDNA and Agilent microarrays: normalized log2 ratio of the sample vs. the reference (UHR)) was transformed into a log2 ratio relative to the median level of expression of that gene across all the samples within the data set of the given platform. The experimental dendrogram displays the clustering of the tumors into distinct subgroups. Branches are color-coded according to the subtype with which the corresponding tumor sample showed the highest correlation. Tumors with low correlation (

    Journal: BMC Genomics

    Article Title: Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms

    doi: 10.1186/1471-2164-7-127

    Figure Lengend Snippet: Validation of the luminal A and basal-like subtypes using three microarray platforms . (A) Unsupervised hierarchical clustering of 20 breast tumor tissues analyzed by Applied Biosystems (two replicates per sample), Stanford cDNA and Agilent arrays using the 510 mapped intrinsic genes. The data from each platform were first transformed independently and then combined for clustering: the level of expression of each gene in each sample (Applied Biosystems microarrays: normalized signal intensity; Stanford cDNA and Agilent microarrays: normalized log2 ratio of the sample vs. the reference (UHR)) was transformed into a log2 ratio relative to the median level of expression of that gene across all the samples within the data set of the given platform. The experimental dendrogram displays the clustering of the tumors into distinct subgroups. Branches are color-coded according to the subtype with which the corresponding tumor sample showed the highest correlation. Tumors with low correlation (

    Article Snippet: Agilent whole human genome microarray analysis The Agilent Whole Human Genome Oligo Microarray contains 44,000 60-mer oligonucleotide probes representing 41,000 unique genes and transcripts [ ].

    Techniques: Microarray, Transformation Assay, Expressing

    Hierarchical clustering analysis of expression data from the TaqMan ® assays and the three microarray platforms across the 85 marker genes . The same tumor sample analyzed by the three microarray platforms and the TaqMan ® Gene Expression assays were clustered together except for one sample (MicMa185). For the Applied Biosystems microarrays, the mean expression values of the two microarray replicates were presented. The transformed z-scores were represented using a red-black-green color scale as shown in the key (green: below mean; black: equal to mean; red: above mean).

    Journal: BMC Genomics

    Article Title: Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms

    doi: 10.1186/1471-2164-7-127

    Figure Lengend Snippet: Hierarchical clustering analysis of expression data from the TaqMan ® assays and the three microarray platforms across the 85 marker genes . The same tumor sample analyzed by the three microarray platforms and the TaqMan ® Gene Expression assays were clustered together except for one sample (MicMa185). For the Applied Biosystems microarrays, the mean expression values of the two microarray replicates were presented. The transformed z-scores were represented using a red-black-green color scale as shown in the key (green: below mean; black: equal to mean; red: above mean).

    Article Snippet: Agilent whole human genome microarray analysis The Agilent Whole Human Genome Oligo Microarray contains 44,000 60-mer oligonucleotide probes representing 41,000 unique genes and transcripts [ ].

    Techniques: Expressing, Microarray, Marker, Transformation Assay

    Unsupervised approach to identify breast cancer subtypes . (A) Correlation of breast tumor samples with the previously identified five subtypes of breast tumors. 526 out of 552 previously identified

    Journal: BMC Genomics

    Article Title: Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms

    doi: 10.1186/1471-2164-7-127

    Figure Lengend Snippet: Unsupervised approach to identify breast cancer subtypes . (A) Correlation of breast tumor samples with the previously identified five subtypes of breast tumors. 526 out of 552 previously identified "intrinsic" genes were cross-mapped to Applied Biosystems Human Genome Survey Microarray and used for centroid correlation analysis and hierarchical clustering. Correlations with the centroids of the five subtypes were calculated for each sample from this study (the two microarray replicates for each sample were averaged). Samples were assigned to a subtype with which it showed the highest correlation using a cutoff value of 0.2. (B) Unsupervised hierarchical clustering of 20 breast tumor tissues analyzed by AB arrays using the 526 mapped intrinsic genes (the two microarray replicates for each sample are shown). The level of expression of each gene in each sample, relative to the median level of expression of that gene across all the samples, is represented using a red-black-green color scale as shown in the key (green: below median; black: equal to median; red: above median). (Left panel): Scaled down representation of the entire cluster of the 526 intrinsic genes and 20 tissue samples. (Right panel): Experimental dendrogram displaying the clustering of the tumors into three distinct subgroups. Branches are color-coded according to the subtype with which the corresponding tumor sample showed the highest correlation. Tumors with low correlation (

    Article Snippet: Agilent whole human genome microarray analysis The Agilent Whole Human Genome Oligo Microarray contains 44,000 60-mer oligonucleotide probes representing 41,000 unique genes and transcripts [ ].

    Techniques: Microarray, Expressing