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multiple long oligonucleotide based microarray platforms from  (Illumina Inc)


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    Illumina Inc multiple long oligonucleotide based microarray platforms from
    Multiple Long Oligonucleotide Based Microarray Platforms From, supplied by Illumina Inc, 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/the+oligonucleotide-based+microarray+platform/oligonucleotide+arrays/pmc03141672-94-13-27
    Average 90 stars, based on 1 article reviews
    multiple long oligonucleotide based microarray platforms from - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Biomarker Discovery:

    Article Title: A Comparative Study of Medium-coverage Genome Sequencing and SNP Array Technology in Identifying Chromosomal Abnormalities to Advance Prenatal and Postnatal Diagnosis.
    Article Snippet: .. Hayes JL, Tzika A, Thygesen H, Berri S, Wood HM, Hewitt S, Pendlebury M, Coates A, 379 Willoughby L, Watson CM, Rabbitts P, Roberts P, Taylor GR: Diagnosis of copy number 380 variation by Illumina next generation sequencing is comparable in performance to 381 oligonucleotide array comparative genomic hybridisation. .. Hayes JL, Tzika A, Thygesen H, Berri S, Wood HM, Hewitt S, Pendlebury M, Coates A, 379 Willoughby L, Watson CM, Rabbitts P, Roberts P, Taylor GR: Diagnosis of copy number 380 variation by Illumina next generation sequencing is comparable in performance to 381 oligonucleotide array comparative genomic hybridisation.

    Next-Generation Sequencing:

    Article Title: A Comparative Study of Medium-coverage Genome Sequencing and SNP Array Technology in Identifying Chromosomal Abnormalities to Advance Prenatal and Postnatal Diagnosis.
    Article Snippet: .. Hayes JL, Tzika A, Thygesen H, Berri S, Wood HM, Hewitt S, Pendlebury M, Coates A, 379 Willoughby L, Watson CM, Rabbitts P, Roberts P, Taylor GR: Diagnosis of copy number 380 variation by Illumina next generation sequencing is comparable in performance to 381 oligonucleotide array comparative genomic hybridisation. .. Hayes JL, Tzika A, Thygesen H, Berri S, Wood HM, Hewitt S, Pendlebury M, Coates A, 379 Willoughby L, Watson CM, Rabbitts P, Roberts P, Taylor GR: Diagnosis of copy number 380 variation by Illumina next generation sequencing is comparable in performance to 381 oligonucleotide array comparative genomic hybridisation.

    Hybridization:

    Article Title: A Comparative Study of Medium-coverage Genome Sequencing and SNP Array Technology in Identifying Chromosomal Abnormalities to Advance Prenatal and Postnatal Diagnosis.
    Article Snippet: .. Hayes JL, Tzika A, Thygesen H, Berri S, Wood HM, Hewitt S, Pendlebury M, Coates A, 379 Willoughby L, Watson CM, Rabbitts P, Roberts P, Taylor GR: Diagnosis of copy number 380 variation by Illumina next generation sequencing is comparable in performance to 381 oligonucleotide array comparative genomic hybridisation. .. Hayes JL, Tzika A, Thygesen H, Berri S, Wood HM, Hewitt S, Pendlebury M, Coates A, 379 Willoughby L, Watson CM, Rabbitts P, Roberts P, Taylor GR: Diagnosis of copy number 380 variation by Illumina next generation sequencing is comparable in performance to 381 oligonucleotide array comparative genomic hybridisation.

    Microarray:

    Article Title: Targeted Transcriptome and <i>KRAS</i> Mutation Analysis Improve the Diagnostic Performance of EUS-FNA Biopsies in Pancreatic Cancer
    Article Snippet: Oligonucleotide microarray data processing Raw affymetrix oligonucleotidemicroarray data (datasets E-MEXP1121/E-MEXP-950, GSE15471, and GSE28735) were processed using the oligo package for R (29) using updated probeset definitions from Custom CDF v23 downloaded from http://brainarray.mbni.med. umich.edu/Brainarray/Database/CustomCDF/23.0.0/ensg.asp (30) and RMA-normalized as implemented in the oligo package (29). .. Raw Illumina oligonucleotide microarray data (datasets GSE101462, GSE101448) were vsn-normalized using the vsn package for R (31). ..

    Variant Assay:

    Article Title: Deep mutational scanning of proteins in mammalian cells.
    Article Snippet: .. Single-site saturation variant libraries are achieved through randomization of the corresponding single codons in degenerate oligonucleotides17,25,50 or through specific singlecodon substitutions in a designed oligonucleotide library synthesized on an array.32,49,65 In degenerate oligonucleotides, different modes of codon randomization influence the representation of each amino acid substitution linked to the degeneracy of the genetic code.74,75 In oligonucleotide arrays, each amino acid substitution is usually equally represented through one codon substitution, and additionally, codon usage can guide the choice of this codon.32 However, it could be more informative and comprehensive to look at all codon substitutions in studies related to translation, folding, and stability.76 Another advantage of oligonucleotide arrays involves the option to introduce insertions and deletions.15,36,49 Because oligonucleotide synthesis is prone to error with increasing length (100–200 bp), longer variable regions need to be subdivided into multiple oligonucleotide arrays that are usually separately synthesized and integrated.32 In addition, this allows for the generation of sublibraries covering partial variable regions compatible with Illumina sequencing read length. ..

    Synthesized:

    Article Title: Deep mutational scanning of proteins in mammalian cells.
    Article Snippet: .. Single-site saturation variant libraries are achieved through randomization of the corresponding single codons in degenerate oligonucleotides17,25,50 or through specific singlecodon substitutions in a designed oligonucleotide library synthesized on an array.32,49,65 In degenerate oligonucleotides, different modes of codon randomization influence the representation of each amino acid substitution linked to the degeneracy of the genetic code.74,75 In oligonucleotide arrays, each amino acid substitution is usually equally represented through one codon substitution, and additionally, codon usage can guide the choice of this codon.32 However, it could be more informative and comprehensive to look at all codon substitutions in studies related to translation, folding, and stability.76 Another advantage of oligonucleotide arrays involves the option to introduce insertions and deletions.15,36,49 Because oligonucleotide synthesis is prone to error with increasing length (100–200 bp), longer variable regions need to be subdivided into multiple oligonucleotide arrays that are usually separately synthesized and integrated.32 In addition, this allows for the generation of sublibraries covering partial variable regions compatible with Illumina sequencing read length. ..

    Introduce:

    Article Title: Deep mutational scanning of proteins in mammalian cells.
    Article Snippet: .. Single-site saturation variant libraries are achieved through randomization of the corresponding single codons in degenerate oligonucleotides17,25,50 or through specific singlecodon substitutions in a designed oligonucleotide library synthesized on an array.32,49,65 In degenerate oligonucleotides, different modes of codon randomization influence the representation of each amino acid substitution linked to the degeneracy of the genetic code.74,75 In oligonucleotide arrays, each amino acid substitution is usually equally represented through one codon substitution, and additionally, codon usage can guide the choice of this codon.32 However, it could be more informative and comprehensive to look at all codon substitutions in studies related to translation, folding, and stability.76 Another advantage of oligonucleotide arrays involves the option to introduce insertions and deletions.15,36,49 Because oligonucleotide synthesis is prone to error with increasing length (100–200 bp), longer variable regions need to be subdivided into multiple oligonucleotide arrays that are usually separately synthesized and integrated.32 In addition, this allows for the generation of sublibraries covering partial variable regions compatible with Illumina sequencing read length. ..

    Oligonucleotide Synthesis:

    Article Title: Deep mutational scanning of proteins in mammalian cells.
    Article Snippet: .. Single-site saturation variant libraries are achieved through randomization of the corresponding single codons in degenerate oligonucleotides17,25,50 or through specific singlecodon substitutions in a designed oligonucleotide library synthesized on an array.32,49,65 In degenerate oligonucleotides, different modes of codon randomization influence the representation of each amino acid substitution linked to the degeneracy of the genetic code.74,75 In oligonucleotide arrays, each amino acid substitution is usually equally represented through one codon substitution, and additionally, codon usage can guide the choice of this codon.32 However, it could be more informative and comprehensive to look at all codon substitutions in studies related to translation, folding, and stability.76 Another advantage of oligonucleotide arrays involves the option to introduce insertions and deletions.15,36,49 Because oligonucleotide synthesis is prone to error with increasing length (100–200 bp), longer variable regions need to be subdivided into multiple oligonucleotide arrays that are usually separately synthesized and integrated.32 In addition, this allows for the generation of sublibraries covering partial variable regions compatible with Illumina sequencing read length. ..

    other:

    Article Title: Probe Selection and Expression Index Computation of Affymetrix Exon Arrays
    Article Snippet: A variety of gene expression microarray platforms are used today, including spotted cDNA arrays, Affymetrix GeneChip arrays, Agilent ink-jet arrays and Illumina long-oligonucleotide bead-based arrays , .

    Amplification:

    Article Title: Cell population-specific expression analysis of human cerebellum
    Article Snippet: Two rounds of amplification were carried out with the Ambion MessageAmp II aRNA kit. .. Illumina human oligonucleotide arrays (HumanHT-12) were used according to the manufacturer's instructions, starting with 750 ng of amplified RNA for each sample. .. Array chips were scanned on an Illumina Bead array reader confocal scanner.



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    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