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the oligonucleotide-based microarray platform  (Agilent technologies)


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    Agilent technologies the oligonucleotide-based microarray platform
    The Oligonucleotide Based Microarray Platform, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/oligonucleotide+microarray+based+microarray+platform/pm25499032-48-2-6
    Average 90 stars, based on 1 article reviews
    the oligonucleotide-based microarray platform - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Microarray:

    Article Title: COL3A1, COL5A1 and COL6A2 serve as potential molecular biomarkers for osteoarthritis based on weighted gene co‑expression network analysis bioinformatics analysis
    Article Snippet: .. GSE51588, a whole-genome profiling study was performed on an Agilent microarray platform and analyzed using an Agilent GeneSpring GX11.5 (Agilent Technologies, Inc.), consisted of 40 OA subchondral bone samples and 10 healthy tissue samples for identification of differentially expressed genes (DEGs) in OA subchondral bone. ..

    Article Title: Sex disparities in non-small cell lung cancer: mechanistic insights from a cRaf transgenic disease model
    Article Snippet: .. Agilent microarray platform: We dephosphorylated 100 ng of total RNA and performed 3′ end labelling with the Cy3-pCp dye, purified the samples with Micro Bio-Spin columns, and hybridized the samples onto arrays with the miRNA Microarray System labelling kit V2 according to the manufacturer’s instructions ( https://www.agilent.com/store/en_US/Prod-5190-0456/5190-0456 ). .. The Agilent mouse miRNA microarray (Release 12.0, catalogue ID G4472B) contains 612 mouse mature miRNAs ( https://www.agilent.com/cs/library/usermanuals/public/G4170-90011.pdf ).

    Article Title: PARP1 Characterization as a Potential Biomarker for BCR::ABL1 p190+ Acute Lymphoblastic Leukemia
    Article Snippet: .. Array-CGH (aCGH) experiments were performed on an Agilent microarray platform (Agilent Technologies) with a SurePrint G3 Cancer CGH + SNP Microarray 4 × 180 K slide (Agilent). .. Sample preparation, labelling, and microarray hybridization were performed according to the Agilent CGH Enzymatic Protocol version 7.5.

    Article Title: Unveil Intrahepatic Cholangiocarcinoma Heterogeneity through the Lens of Omics and Multi-Omics Approaches
    Article Snippet: .. Peraldo-Neia et al. [ ] performed gene expression profiling by the Agilent microarray platform in 11 pairs of primary (PR) and recurrent (REC) iCCA tumors collected from the same patient. ..

    Article Title: Occupational exposure to potentially toxic elements alters gene expression profiles in formal and informal Brazilian workers.
    Article Snippet: Chemical elements, such as toxic metals, have previously demonstrated their ability to alter gene expression in humans and other species.. In this study, microarray analysis was used to compare the gene expression profiles of different occupational exposure populations: a) informal workers who perform soldering of jewelry inside their houses (n = 22) in São Paulo (SP) State; and b) formal workers from a steel company (n = 10) in Rio de Janeiro (RJ) state, Brazil.. Control participants were recruited from the same neighborhoods without occupational chemical exposure (n = 19 in SP and n = 8 in RJ).

    Article Title: Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size
    Article Snippet: .. In line with the effectivity of this methodology, recently, a protocol has been developed to specifically examine both indica and japonica whole grains using an Agilent microarray platform [ ]. ..

    Article Title: Microarray evidence that 8-cell human embryos express some hormone family members including oxytocin.
    Article Snippet: Objective This study is to discover hormone pathways active in early cleaving human embryos.. Methods A list of 152 hormones and receptors were compiled to query the microarray database of mRNAs in 8-cell human embryos, two lines of human embryonic stem cells plus human fibroblasts before and after induced pluripotency.. Results Over half of the 152 hormones and receptors were silent on the arrays of all cell types, and more were detected at high or moderate levels on the 8-cell arrays than on the pluripotent cell or fibroblast arrays.

    Purification:

    Article Title: Sex disparities in non-small cell lung cancer: mechanistic insights from a cRaf transgenic disease model
    Article Snippet: .. Agilent microarray platform: We dephosphorylated 100 ng of total RNA and performed 3′ end labelling with the Cy3-pCp dye, purified the samples with Micro Bio-Spin columns, and hybridized the samples onto arrays with the miRNA Microarray System labelling kit V2 according to the manufacturer’s instructions ( https://www.agilent.com/store/en_US/Prod-5190-0456/5190-0456 ). .. The Agilent mouse miRNA microarray (Release 12.0, catalogue ID G4472B) contains 612 mouse mature miRNAs ( https://www.agilent.com/cs/library/usermanuals/public/G4170-90011.pdf ).

    Gene Expression:

    Article Title: Unveil Intrahepatic Cholangiocarcinoma Heterogeneity through the Lens of Omics and Multi-Omics Approaches
    Article Snippet: .. Peraldo-Neia et al. [ ] performed gene expression profiling by the Agilent microarray platform in 11 pairs of primary (PR) and recurrent (REC) iCCA tumors collected from the same patient. ..



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    Image Search Results


    Microarray interplatform analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms used in this study. The pool of 17070 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes at 6 h after EGF treatment considering each of the 3 microarray platforms independently.

    Journal: BMC Genomics

    Article Title: Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

    doi: 10.1186/1471-2164-12-326

    Figure Lengend Snippet: Microarray interplatform analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms used in this study. The pool of 17070 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes at 6 h after EGF treatment considering each of the 3 microarray platforms independently.

    Article Snippet: Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer.

    Techniques: Microarray

    GSEA analysis on significantly regulated gene sets across microarray platforms . Profile of the Running ES Score & Positions of Gene Set Members on the Rank Ordered List using 6 h EGF treatment data according to each of the three microarray platforms. In each panel, the vertical black lines indicate the position of each of the genes of the tested gene set in the reference data set (ranked by average of the three respective EGF versus control log2ratios of replicate experiments). The green curve plots the ES (enrichment score), which is the running sum of the weighted enrichment score obtained from GSEA software. Within each queried gene set, the farther the position of a gene to the left (red) implies a higher correlation with EGF up-regulated genes in the reference platform, and the farther to the right (blue) implies a higher correlation with genes down-regulated upon EGF treatment in the reference platform. Studied gene sets correspond to lists of up- or down-regulated genes in each platform at 6 h of EGF treatment. Significantly enriched data sets are defined according to GSEA default settings (p < 0.001 and a false discovery rate (FDR) < 0.25). R.L.M = ranked list metric.

    Journal: BMC Genomics

    Article Title: Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

    doi: 10.1186/1471-2164-12-326

    Figure Lengend Snippet: GSEA analysis on significantly regulated gene sets across microarray platforms . Profile of the Running ES Score & Positions of Gene Set Members on the Rank Ordered List using 6 h EGF treatment data according to each of the three microarray platforms. In each panel, the vertical black lines indicate the position of each of the genes of the tested gene set in the reference data set (ranked by average of the three respective EGF versus control log2ratios of replicate experiments). The green curve plots the ES (enrichment score), which is the running sum of the weighted enrichment score obtained from GSEA software. Within each queried gene set, the farther the position of a gene to the left (red) implies a higher correlation with EGF up-regulated genes in the reference platform, and the farther to the right (blue) implies a higher correlation with genes down-regulated upon EGF treatment in the reference platform. Studied gene sets correspond to lists of up- or down-regulated genes in each platform at 6 h of EGF treatment. Significantly enriched data sets are defined according to GSEA default settings (p < 0.001 and a false discovery rate (FDR) < 0.25). R.L.M = ranked list metric.

    Article Snippet: Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer.

    Techniques: Microarray, Software

    Microarray versus DGE analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.

    Journal: BMC Genomics

    Article Title: Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

    doi: 10.1186/1471-2164-12-326

    Figure Lengend Snippet: Microarray versus DGE analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.

    Article Snippet: Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer.

    Techniques: Microarray

    Correlation between microarrays and Illumina GA-I sequencing . (A) Comparison of estimated log2ratios from DGE ( Y -axis) and the mean of all microarray platforms ( X -axis). We consider only genes that were interrogated using all platforms and genes with a mean number of counts across lanes greater than 0. Genes with counts greater than 32 reads (colored red or green) or less than (black) 32 reads in at least one sample are shown. (Red dots) Genes called differentially expressed based on DGE data at an 10% FDR by RankProd. (Green dots) Genes not called as differentially expressed but above 32 counts. (Inset box) Correlation between technologies is higher when considering genes above the 32 count detection level (0.57) than when all genes are included (0.49). (B-C) Concordance at the top (CAT) plots of the different platforms with the 500 top genes from a reference platform, shown for Agilent in (B) and DGE in (C). See inset box for color codes identifying each platforms compared to the remaining platform used as reference. (D) Correlation plots with regression lines between log2ratios of the five high content platforms measurements (Y-axis) and quantitative real time PCR results using SYBR green assays (X-axis), based on measurements for 21 genes at the 6 h time point (see Additional file , Table S1).

    Journal: BMC Genomics

    Article Title: Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

    doi: 10.1186/1471-2164-12-326

    Figure Lengend Snippet: Correlation between microarrays and Illumina GA-I sequencing . (A) Comparison of estimated log2ratios from DGE ( Y -axis) and the mean of all microarray platforms ( X -axis). We consider only genes that were interrogated using all platforms and genes with a mean number of counts across lanes greater than 0. Genes with counts greater than 32 reads (colored red or green) or less than (black) 32 reads in at least one sample are shown. (Red dots) Genes called differentially expressed based on DGE data at an 10% FDR by RankProd. (Green dots) Genes not called as differentially expressed but above 32 counts. (Inset box) Correlation between technologies is higher when considering genes above the 32 count detection level (0.57) than when all genes are included (0.49). (B-C) Concordance at the top (CAT) plots of the different platforms with the 500 top genes from a reference platform, shown for Agilent in (B) and DGE in (C). See inset box for color codes identifying each platforms compared to the remaining platform used as reference. (D) Correlation plots with regression lines between log2ratios of the five high content platforms measurements (Y-axis) and quantitative real time PCR results using SYBR green assays (X-axis), based on measurements for 21 genes at the 6 h time point (see Additional file , Table S1).

    Article Snippet: Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer.

    Techniques: Sequencing, Microarray, Real-time Polymerase Chain Reaction, SYBR Green Assay

    Top regulated genes derived from meta-analysis . RankProd analysis of the combination of microarray and Illumina GA-I ultrasequencing data sets. Heatmap of the top 50 up and down-regulated genes detected in all four platforms ordered by Median Fold Change (all have RankProd adjusted p-values < 0.0001). IL11, IL8, PLAUR, ANXA10 and FOS were validated by RT-qPCR showing concordant results (See Additional file , Table S1). The full RankProd matrix from these experiments is accessible in Additional file , Table S5. The list of all 1164 significantly regulated genes (median |FC| > 1.2 and RankProd q-value < 0.05) is given in Additional file , Table S6.

    Journal: BMC Genomics

    Article Title: Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

    doi: 10.1186/1471-2164-12-326

    Figure Lengend Snippet: Top regulated genes derived from meta-analysis . RankProd analysis of the combination of microarray and Illumina GA-I ultrasequencing data sets. Heatmap of the top 50 up and down-regulated genes detected in all four platforms ordered by Median Fold Change (all have RankProd adjusted p-values < 0.0001). IL11, IL8, PLAUR, ANXA10 and FOS were validated by RT-qPCR showing concordant results (See Additional file , Table S1). The full RankProd matrix from these experiments is accessible in Additional file , Table S5. The list of all 1164 significantly regulated genes (median |FC| > 1.2 and RankProd q-value < 0.05) is given in Additional file , Table S6.

    Article Snippet: Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer.

    Techniques: Derivative Assay, Microarray, Quantitative RT-PCR