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Agilent technologies custom oligonucleotide microarrays
Custom Oligonucleotide Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 87/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/custom oligonucleotide microarrays/product/Agilent technologies
Average 87 stars, based on 7 article reviews
Price from $9.99 to $1999.99
custom oligonucleotide microarrays - by Bioz Stars, 2019-10
87/100 stars

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Related Articles

Functional Assay:

Article Title: High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes
Article Snippet: The general idea of a synthetic oligo library, a molecular selection, and a microarray based readout could be reconfigured into a variety of functional assays. .. Oligonucleotide pools can be inexpensively synthesized from commercial sources (e.g., Atactic makes 4000 sequences for approximately $700) or even mechanically scoured from custom oligonucleotide microarray (e.g., Agilent microarray yields 240,000 sequences at a cost of $450).

Amplification:

Article Title: Genomic and Genotoxic Responses to Controlled Weathered-Oil Exposures Confirm and Extend Field Studies on Impacts of the Deepwater Horizon Oil Spill on Native Killifish
Article Snippet: Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999). .. RNA extraction and microarray hybridizations followed the same methods as those reported in Whitehead et al. .

Article Title: Mechanisms of Resistance to Decitabine in the Myelodysplastic Syndrome
Article Snippet: Methylated CpG island amplification was performed as described . .. Amplicons from patients with MDS after relapse were labeled with the Cy5 dye and cohybridized against amplicons from patients at diagnosis labeled with the Cy3 dye on Agilent Technologies 4×44 K custom DNA microarrays (Agilent, Santa Clara, CA) as described previously .

Synthesized:

Article Title: High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes
Article Snippet: MEGAshift is an affordable means to biochemically characterize a large sequence pool. .. Oligonucleotide pools can be inexpensively synthesized from commercial sources (e.g., Atactic makes 4000 sequences for approximately $700) or even mechanically scoured from custom oligonucleotide microarray (e.g., Agilent microarray yields 240,000 sequences at a cost of $450). .. These pools represent a one-time expense as the oligo library can be propagated by PCR amplification in multiple experiments.

Article Title: Exploring the sequence space of a DNA aptamer using microarrays
Article Snippet: To evaluate reproducibility, incubations at 100 nM protein concentration have been performed three times (on three different arrays), and the array-to-array variability was also within 10% of the mean signals. .. DNA sequences on custom DNA arrays from Agilent can be synthesized up to 60 nt in length. .. Since the IgE-binding aptamer is only 37 nt long , the initial investigation of this aptamer immobilized on the surface of the microarray focused on establishing the optimum length of the linker separating the aptamer from the surface.

Article Title: Array-based Discovery of Aptamer Pairs
Article Snippet: We designed and ordered custom DNA microarrays through Agilent, where each slide consisted of eight identical subarrays of 15 000 individual features. .. The array design was based on aptamer sequences identified from high-throughput sequencing.

Real-time Polymerase Chain Reaction:

Article Title: Label-Free Quantification of MicroRNAs Using Ligase-Assisted Sandwich Hybridization on a DNA Microarray
Article Snippet: To quantify miRNAs on a DNA microarray, we utilized a commercial custom DNA microarray from Agilent Corporation. miRNAs in two total RNA samples derived from different types of blood from healthy humans were quantified as described in Materials and Methods. .. The expression levels of miR-143, miR-21, miR-16 and miR-92a in each total RNA sample measured by LASH assay were similar to respective levels measured by qRT-PCR ( , ).

Microarray:

Article Title: High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes
Article Snippet: MEGAshift is an affordable means to biochemically characterize a large sequence pool. .. Oligonucleotide pools can be inexpensively synthesized from commercial sources (e.g., Atactic makes 4000 sequences for approximately $700) or even mechanically scoured from custom oligonucleotide microarray (e.g., Agilent microarray yields 240,000 sequences at a cost of $450). .. These pools represent a one-time expense as the oligo library can be propagated by PCR amplification in multiple experiments.

Article Title: An RRM–ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion
Article Snippet: The RNA pool generation, RNAcompete pulldown assays, and microarray hybridizations were performed as previously described ( , ). .. Briefly, RNAcompete experiments employed defined RNA pools that are generated from 244 K Agilent custom DNA microarrays.

Article Title: Co-occurrence of a maternally inherited DNMT3A duplication and a paternally inherited pathogenic variant in EZH2 in a child with growth retardation and severe short stature: atypical Weaver syndrome or evidence of a DNMT3A dosage effect?
Article Snippet: The protocol was approved by the institutional review board of the Mayo Clinic. .. CMA was performed using a custom oligonucleotide microarray (Agilent 180K probe platform) representing a uniform design developed through the International Standards for Cytogenomic Arrays consortium. .. The genome-wide functional resolution of this array is approximately 100 kilobases (kb), with higher resolution in targeted genes and regions of known clinical significance.

Article Title: Label-Free Quantification of MicroRNAs Using Ligase-Assisted Sandwich Hybridization on a DNA Microarray
Article Snippet: These results suggest that the LASH assay is able to quantify endogenous miRNA exported from living cells. .. To quantify miRNAs on a DNA microarray, we utilized a commercial custom DNA microarray from Agilent Corporation. miRNAs in two total RNA samples derived from different types of blood from healthy humans were quantified as described in Materials and Methods. .. The expression levels of miR-143, miR-21, miR-16 and miR-92a in each total RNA sample measured by LASH assay were similar to respective levels measured by qRT-PCR ( , ).

Article Title: Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways
Article Snippet: Expression levels of target genes were normalized to the expression level of the 16S rRNA gene. .. Transcriptome analysis was performed using custom DNA microarrays (8 × 15K; Agilent Technologies) previously designed based on the annotated genome sequences of S. oneidensis MR-1 according to the manufacturer’s protocol for gene expression arrays for prokaryotes (Agilent One-Color Microarray-Based Prokaryote Analysis, version 1.4, http://www.chem.agilent.com ). .. For transcriptome analysis of the WT strain, five biological replicates were prepared from independent ECs (n = 5).

Article Title: Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts
Article Snippet: 20 Agilent custom oligonucleotide arrays, hybridization buffers, and wash buffers consistently yield high-quality data. .. 20 Agilent custom oligonucleotide arrays, hybridization buffers, and wash buffers consistently yield high-quality data.

Article Title: Genomic and Genotoxic Responses to Controlled Weathered-Oil Exposures Confirm and Extend Field Studies on Impacts of the Deepwater Horizon Oil Spill on Native Killifish
Article Snippet: Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999). .. Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999).

Article Title: Transcriptome profiling of a curdlan-producing Agrobacterium reveals conserved regulatory mechanisms of exopolysaccharide biosynthesis
Article Snippet: The RNA was converted to cDNA and labeled with either Cy-3 or Cy-5 using the Fairplay III Microarray Labeling kit from Agilent. .. The microarray is an 8 × 15 k custom DNA microarray from Agilent with probes designed using Agilent's eArray program. .. The eArray program designed probes for 5,580 of the 5,585 predicted genes in the ATCC 31749 genome with two technical replicates for each gene.

Article Title: Smc5/6 Coordinates Formation and Resolution of Joint Molecules with Chromosome Morphology to Ensure Meiotic Divisions
Article Snippet: Briefly, Smc5 crosslinked chromatin was immunoprecipitated with 2 µl anti-myc 9E11 (Abcam) or 20 µl anti-V5 beads (Sigma-Aldrich). .. Immunoprecipitated and input DNA samples were cohybridized to a custom DNA microarray (Agilent) and data were normalized as previously described. .. The relative enrichment of Smc5 to Rec8 and Smc5 in spo11 versus SPO11 is the ratio of the values in each of the two datasets indicated.

Article Title: Multiple orbital neurofibromas, painful peripheral nerve tumors, distinctive face and marfanoid habitus: a new syndrome
Article Snippet: In addition, analysis of exons 1–9 of the PTEN gene showed no alteration. .. An array comparative genomic hybridization (CGH) assay using a custom oligonucleotide microarray (Agilent Technologies Inc., Santa Clara, CA, USA) showed duplication of 14 nucleotide probes at 17q12 spanning approximately 925 kilobases; parental studies revealed the same chromosomal finding in the patient's unaffected mother. .. Peripheral nerve tumors are hallmarks of several well-known familial tumor syndromes, including NF1 and NF2, familial and sporadic schwannomatosis, and MEN2B.

Article Title: Mechanisms of Resistance to Decitabine in the Myelodysplastic Syndrome
Article Snippet: Paragraph title: Methylated CpG island microarray (MCAM) ... Amplicons from patients with MDS after relapse were labeled with the Cy5 dye and cohybridized against amplicons from patients at diagnosis labeled with the Cy3 dye on Agilent Technologies 4×44 K custom DNA microarrays (Agilent, Santa Clara, CA) as described previously .

Article Title: Transcriptional Analysis of Lactobacillus brevis to N-Butanol and Ferulic Acid Stress Responses
Article Snippet: Paragraph title: Labeled cDNA Generation and Microarray Hybridization ... Custom cDNA microarrays (Agilent) containing 15,209 probes (excluding positive and negative controls) were designed using the software package Picky to maximize probe specificity and sensitivity under hybridization conditions with the following parameters.

Expressing:

Article Title: Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds
Article Snippet: Custom DNA microarrays were obtained from Agilent Technologies (Waldbronn, Germany). .. Agilent's eArray platform was used to design oligonucleotide probes and assemble the custom 4-by-44,000 60-mer microarray.

Article Title: High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes
Article Snippet: Oligonucleotide pools can be inexpensively synthesized from commercial sources (e.g., Atactic makes 4000 sequences for approximately $700) or even mechanically scoured from custom oligonucleotide microarray (e.g., Agilent microarray yields 240,000 sequences at a cost of $450). .. Microarrays can be stripped and reused several times, and the results could easily be analyzed by sequencing if microarray scanners are unavailable ( ).

Article Title: A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria
Article Snippet: Transcriptomes of C. glutamicum ATCC 13032 were comparisons of cells treated with or without 0.6 mM mitomycin C after 1, 3, 6 and 9 h after addition of mitomycin C. The custom DNA microarrays were obtained from Agilent Technologies (Waldbronn, Germany). .. Agilent's eArray platform was used to design oligonucleotide probes with the best probe methodology and assemble custom 4×44K 60mer microarray designs ( https://earray.chem.agilent.com/earray/ ).

Article Title: Label-Free Quantification of MicroRNAs Using Ligase-Assisted Sandwich Hybridization on a DNA Microarray
Article Snippet: To quantify miRNAs on a DNA microarray, we utilized a commercial custom DNA microarray from Agilent Corporation. miRNAs in two total RNA samples derived from different types of blood from healthy humans were quantified as described in Materials and Methods. .. Correlation factors between qPCR and LASH assay were calculated to be 0.99 for [A] and 0.95 for [B] ( ).

Article Title: Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways
Article Snippet: Expression levels of target genes were normalized to the expression level of the 16S rRNA gene. .. Transcriptome analysis was performed using custom DNA microarrays (8 × 15K; Agilent Technologies) previously designed based on the annotated genome sequences of S. oneidensis MR-1 according to the manufacturer’s protocol for gene expression arrays for prokaryotes (Agilent One-Color Microarray-Based Prokaryote Analysis, version 1.4, http://www.chem.agilent.com ). .. For transcriptome analysis of the WT strain, five biological replicates were prepared from independent ECs (n = 5).

Article Title: Genomic and Genotoxic Responses to Controlled Weathered-Oil Exposures Confirm and Extend Field Studies on Impacts of the Deepwater Horizon Oil Spill on Native Killifish
Article Snippet: Genome-wide gene expression profiling offers a global discovery-based approach for revealing the mechanisms that animals utilize to respond to environmental stressors. .. Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999). .. This same microarray design was used in killifish PCB-126 exposure experiments and field-based DWH oil exposure experiments , , such that data from these studies are directly comparable.

Article Title: Smc5/6 Coordinates Formation and Resolution of Joint Molecules with Chromosome Morphology to Ensure Meiotic Divisions
Article Snippet: Immunoprecipitated and input DNA samples were cohybridized to a custom DNA microarray (Agilent) and data were normalized as previously described. .. Immunoprecipitated and input DNA samples were cohybridized to a custom DNA microarray (Agilent) and data were normalized as previously described.

Article Title: Dynamic Nucleosome Organization at hox Promoters during Zebrafish Embryogenesis
Article Snippet: These time points were chosen since zygotic gene expression is initiated at 3–4 hpf in the zebrafish . .. Mononucleosome sized fragments were gel-purified and hybridized to an Agilent custom DNA array tiled with 50 bp oligonucleotides positioned every 20 bp across the seven zebrafish hox clusters.

Genome Wide:

Article Title: Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds
Article Snippet: Custom DNA microarrays were obtained from Agilent Technologies (Waldbronn, Germany). .. Agilent's eArray platform was used to design oligonucleotide probes and assemble the custom 4-by-44,000 60-mer microarray.

Article Title: A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria
Article Snippet: Transcriptomes of C. glutamicum ATCC 13032 were comparisons of cells treated with or without 0.6 mM mitomycin C after 1, 3, 6 and 9 h after addition of mitomycin C. The custom DNA microarrays were obtained from Agilent Technologies (Waldbronn, Germany). .. Agilent's eArray platform was used to design oligonucleotide probes with the best probe methodology and assemble custom 4×44K 60mer microarray designs ( https://earray.chem.agilent.com/earray/ ).

Article Title: Genomic and Genotoxic Responses to Controlled Weathered-Oil Exposures Confirm and Extend Field Studies on Impacts of the Deepwater Horizon Oil Spill on Native Killifish
Article Snippet: Paragraph title: Genome-wide gene expression ... Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999).

Article Title: Smc5/6 Coordinates Formation and Resolution of Joint Molecules with Chromosome Morphology to Ensure Meiotic Divisions
Article Snippet: Paragraph title: Genome-wide Smc5 DNA binding and microarray analysis ... Immunoprecipitated and input DNA samples were cohybridized to a custom DNA microarray (Agilent) and data were normalized as previously described.

Derivative Assay:

Article Title: Label-Free Quantification of MicroRNAs Using Ligase-Assisted Sandwich Hybridization on a DNA Microarray
Article Snippet: These results suggest that the LASH assay is able to quantify endogenous miRNA exported from living cells. .. To quantify miRNAs on a DNA microarray, we utilized a commercial custom DNA microarray from Agilent Corporation. miRNAs in two total RNA samples derived from different types of blood from healthy humans were quantified as described in Materials and Methods. .. The expression levels of miR-143, miR-21, miR-16 and miR-92a in each total RNA sample measured by LASH assay were similar to respective levels measured by qRT-PCR ( , ).

Hybridization:

Article Title: Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts
Article Snippet: If fewer than eight labeling reactions are to be performed, any unused dye can be desiccated and stored at 4 °C in the dark. .. 20 Agilent custom oligonucleotide arrays, hybridization buffers, and wash buffers consistently yield high-quality data. .. Be sure that equal amounts of the input and IP sample are used for hybridization.

Article Title: Genomic and Genotoxic Responses to Controlled Weathered-Oil Exposures Confirm and Extend Field Studies on Impacts of the Deepwater Horizon Oil Spill on Native Killifish
Article Snippet: Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999). .. RNA extraction and microarray hybridizations followed the same methods as those reported in Whitehead et al. .

Article Title: Multiple orbital neurofibromas, painful peripheral nerve tumors, distinctive face and marfanoid habitus: a new syndrome
Article Snippet: In addition, analysis of exons 1–9 of the PTEN gene showed no alteration. .. An array comparative genomic hybridization (CGH) assay using a custom oligonucleotide microarray (Agilent Technologies Inc., Santa Clara, CA, USA) showed duplication of 14 nucleotide probes at 17q12 spanning approximately 925 kilobases; parental studies revealed the same chromosomal finding in the patient's unaffected mother. .. Peripheral nerve tumors are hallmarks of several well-known familial tumor syndromes, including NF1 and NF2, familial and sporadic schwannomatosis, and MEN2B.

Article Title: Mechanisms of Resistance to Decitabine in the Myelodysplastic Syndrome
Article Snippet: Amplicons from patients with MDS after relapse were labeled with the Cy5 dye and cohybridized against amplicons from patients at diagnosis labeled with the Cy3 dye on Agilent Technologies 4×44 K custom DNA microarrays (Agilent, Santa Clara, CA) as described previously . .. Amplicons from patients with MDS after relapse were labeled with the Cy5 dye and cohybridized against amplicons from patients at diagnosis labeled with the Cy3 dye on Agilent Technologies 4×44 K custom DNA microarrays (Agilent, Santa Clara, CA) as described previously .

Article Title: Transcriptional Analysis of Lactobacillus brevis to N-Butanol and Ferulic Acid Stress Responses
Article Snippet: Cy3 and Cy5 (GE Healthcare) or Alexa Fluor (Invitrogen) dyes were used to label the cDNA samples. .. Custom cDNA microarrays (Agilent) containing 15,209 probes (excluding positive and negative controls) were designed using the software package Picky to maximize probe specificity and sensitivity under hybridization conditions with the following parameters. .. All probes are sixty base pair oligomers with 100% similarity to their corresponding target sequence.

Flow Cytometry:

Article Title: Agrobacterium tumefaciens ExoR Controls Acid Response Genes and Impacts Exopolysaccharide Synthesis, Horizontal Gene Transfer, and Virulence Gene Expression
Article Snippet: To identify all genes directly and indirectly affected by ExoR, we compared the transcriptome of wild-type C58 to a Δ exoR mutant using Agilent custom oligonucleotide microarrays. .. The distribution of these 491 genes is roughly proportional to the percentage of the genome represented by each replicon: 262 genes (53.4%) are located on the circular chromosome (51.9% of genome), 173 genes (35.2%) on the linear chromosome (34.5% of genome), 40 genes (8.1%) on the At plasmid (9.9% of genome), and 16 genes (3.3%) on the Ti plasmid (3.6% of genome).

Gas Chromatography:

Article Title: Transcriptional Analysis of Lactobacillus brevis to N-Butanol and Ferulic Acid Stress Responses
Article Snippet: Custom cDNA microarrays (Agilent) containing 15,209 probes (excluding positive and negative controls) were designed using the software package Picky to maximize probe specificity and sensitivity under hybridization conditions with the following parameters. .. Custom cDNA microarrays (Agilent) containing 15,209 probes (excluding positive and negative controls) were designed using the software package Picky to maximize probe specificity and sensitivity under hybridization conditions with the following parameters.

Concentration Assay:

Article Title: Genomic and Genotoxic Responses to Controlled Weathered-Oil Exposures Confirm and Extend Field Studies on Impacts of the Deepwater Horizon Oil Spill on Native Killifish
Article Snippet: Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999). .. This same microarray design was used in killifish PCB-126 exposure experiments and field-based DWH oil exposure experiments , , such that data from these studies are directly comparable.

Article Title: Transcriptome profiling of a curdlan-producing Agrobacterium reveals conserved regulatory mechanisms of exopolysaccharide biosynthesis
Article Snippet: RNA concentration was calculated from OD260 , measured using the SpectraMax M5 microplate reader with Corning's UV-transparent 96-well microplates. .. The microarray is an 8 × 15 k custom DNA microarray from Agilent with probes designed using Agilent's eArray program.

Article Title: Transcriptional Analysis of Lactobacillus brevis to N-Butanol and Ferulic Acid Stress Responses
Article Snippet: Custom cDNA microarrays (Agilent) containing 15,209 probes (excluding positive and negative controls) were designed using the software package Picky to maximize probe specificity and sensitivity under hybridization conditions with the following parameters. .. The minimum acceptable between the probe target and other sequences was set at 15 C, with a GC content range between 30–70%.

Generated:

Article Title: An RRM–ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion
Article Snippet: The RNA pool generation, RNAcompete pulldown assays, and microarray hybridizations were performed as previously described ( , ). .. Briefly, RNAcompete experiments employed defined RNA pools that are generated from 244 K Agilent custom DNA microarrays. .. Pool design is based on a de Bruijn sequence of order 11 that was subsequently modified to minimize secondary structure in the designed sequences and minimize intramolecular RNA cross-hybridization.

other:

Article Title: Temporal and fluoride control of secondary metabolism regulates cellular organofluorine biosynthesis
Article Snippet: Custom DNA microarrays (Agilent Technologies) were designed using eArray for a total of 15,744 60–mer probes.

Imaging:

Article Title: Transcriptome profiling of a curdlan-producing Agrobacterium reveals conserved regulatory mechanisms of exopolysaccharide biosynthesis
Article Snippet: The microarray is an 8 × 15 k custom DNA microarray from Agilent with probes designed using Agilent's eArray program. .. The microarray is an 8 × 15 k custom DNA microarray from Agilent with probes designed using Agilent's eArray program.

Protein Concentration:

Article Title: Exploring the sequence space of a DNA aptamer using microarrays
Article Snippet: DNA sequences on custom DNA arrays from Agilent can be synthesized up to 60 nt in length. .. DNA sequences on custom DNA arrays from Agilent can be synthesized up to 60 nt in length.

Sequencing:

Article Title: High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes
Article Snippet: MEGAshift is an affordable means to biochemically characterize a large sequence pool. .. Oligonucleotide pools can be inexpensively synthesized from commercial sources (e.g., Atactic makes 4000 sequences for approximately $700) or even mechanically scoured from custom oligonucleotide microarray (e.g., Agilent microarray yields 240,000 sequences at a cost of $450).

Article Title: Multiple orbital neurofibromas, painful peripheral nerve tumors, distinctive face and marfanoid habitus: a new syndrome
Article Snippet: Sequencing of exons 2–11 of the PRKAR1A gene (GeneDx Laboratory, Gaithersburg, MD, USA) revealed no mutations. .. An array comparative genomic hybridization (CGH) assay using a custom oligonucleotide microarray (Agilent Technologies Inc., Santa Clara, CA, USA) showed duplication of 14 nucleotide probes at 17q12 spanning approximately 925 kilobases; parental studies revealed the same chromosomal finding in the patient's unaffected mother.

Article Title: Array-based Discovery of Aptamer Pairs
Article Snippet: We designed and ordered custom DNA microarrays through Agilent, where each slide consisted of eight identical subarrays of 15 000 individual features. .. The array design was based on aptamer sequences identified from high-throughput sequencing.

Binding Assay:

Article Title: High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes
Article Snippet: MEGAshift is not limited to binding assays. .. Oligonucleotide pools can be inexpensively synthesized from commercial sources (e.g., Atactic makes 4000 sequences for approximately $700) or even mechanically scoured from custom oligonucleotide microarray (e.g., Agilent microarray yields 240,000 sequences at a cost of $450).

Article Title: Exploring the sequence space of a DNA aptamer using microarrays
Article Snippet: DNA sequences on custom DNA arrays from Agilent can be synthesized up to 60 nt in length. .. Aptamer sequences were designed to contain a linker from 0 to 23 Ts on the 3′ end separating the aptamer from the surface (aptamer attachment to the surface is through the 3′ end, as the DNA strands are synthesized in the 3′–5′ direction).

Article Title: Smc5/6 Coordinates Formation and Resolution of Joint Molecules with Chromosome Morphology to Ensure Meiotic Divisions
Article Snippet: Paragraph title: Genome-wide Smc5 DNA binding and microarray analysis ... Immunoprecipitated and input DNA samples were cohybridized to a custom DNA microarray (Agilent) and data were normalized as previously described.

Methylation:

Article Title: Mechanisms of Resistance to Decitabine in the Myelodysplastic Syndrome
Article Snippet: Paragraph title: Methylated CpG island microarray (MCAM) ... Amplicons from patients with MDS after relapse were labeled with the Cy5 dye and cohybridized against amplicons from patients at diagnosis labeled with the Cy3 dye on Agilent Technologies 4×44 K custom DNA microarrays (Agilent, Santa Clara, CA) as described previously .

Mutagenesis:

Article Title: Agrobacterium tumefaciens ExoR Controls Acid Response Genes and Impacts Exopolysaccharide Synthesis, Horizontal Gene Transfer, and Virulence Gene Expression
Article Snippet: Microarray data have been deposited into the Gene Expression Omnibus (GEO) ( ) database under accession number . .. To identify all genes directly and indirectly affected by ExoR, we compared the transcriptome of wild-type C58 to a Δ exoR mutant using Agilent custom oligonucleotide microarrays. .. This analysis identified 491 genes that were differentially expressed between strain C58 and the Δ exoR mutant, with a P value of less than 0.05 and an M value of at least ±0.5, indicating a minimum fold change (FC) of 1.4 (see Fig. S1 in the supplemental material).

Isolation:

Article Title: Transcriptome profiling of a curdlan-producing Agrobacterium reveals conserved regulatory mechanisms of exopolysaccharide biosynthesis
Article Snippet: Paragraph title: RNA isolation and microarray processing ... The microarray is an 8 × 15 k custom DNA microarray from Agilent with probes designed using Agilent's eArray program.

Article Title: Dynamic Nucleosome Organization at hox Promoters during Zebrafish Embryogenesis
Article Snippet: Nucleosome densities were determined by micrococcal nuclease (MNase) digestion of cross-linked chromatin isolated from staged embryos (adapted from ). .. Mononucleosome sized fragments were gel-purified and hybridized to an Agilent custom DNA array tiled with 50 bp oligonucleotides positioned every 20 bp across the seven zebrafish hox clusters.

DNA Array:

Article Title: Dynamic Nucleosome Organization at hox Promoters during Zebrafish Embryogenesis
Article Snippet: Nucleosome densities were determined by micrococcal nuclease (MNase) digestion of cross-linked chromatin isolated from staged embryos (adapted from ). .. Mononucleosome sized fragments were gel-purified and hybridized to an Agilent custom DNA array tiled with 50 bp oligonucleotides positioned every 20 bp across the seven zebrafish hox clusters. .. Randomly fragmented mononucleosome sized genomic DNA (gDNA) was co-hybridized as a control.

Labeling:

Article Title: Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts
Article Snippet: 20 Agilent custom oligonucleotide arrays, hybridization buffers, and wash buffers consistently yield high-quality data. .. 20 Agilent custom oligonucleotide arrays, hybridization buffers, and wash buffers consistently yield high-quality data.

Article Title: Transcriptome profiling of a curdlan-producing Agrobacterium reveals conserved regulatory mechanisms of exopolysaccharide biosynthesis
Article Snippet: The RNA was converted to cDNA and labeled with either Cy-3 or Cy-5 using the Fairplay III Microarray Labeling kit from Agilent. .. The microarray is an 8 × 15 k custom DNA microarray from Agilent with probes designed using Agilent's eArray program.

Article Title: Mechanisms of Resistance to Decitabine in the Myelodysplastic Syndrome
Article Snippet: Methylated CpG island amplification was performed as described . .. Amplicons from patients with MDS after relapse were labeled with the Cy5 dye and cohybridized against amplicons from patients at diagnosis labeled with the Cy3 dye on Agilent Technologies 4×44 K custom DNA microarrays (Agilent, Santa Clara, CA) as described previously . .. Dye swaps were preformed for comparison.

Article Title: Transcriptional Analysis of Lactobacillus brevis to N-Butanol and Ferulic Acid Stress Responses
Article Snippet: Paragraph title: Labeled cDNA Generation and Microarray Hybridization ... Custom cDNA microarrays (Agilent) containing 15,209 probes (excluding positive and negative controls) were designed using the software package Picky to maximize probe specificity and sensitivity under hybridization conditions with the following parameters.

Purification:

Article Title: Genomic and Genotoxic Responses to Controlled Weathered-Oil Exposures Confirm and Extend Field Studies on Impacts of the Deepwater Horizon Oil Spill on Native Killifish
Article Snippet: Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999). .. RNA extraction and microarray hybridizations followed the same methods as those reported in Whitehead et al. .

Article Title: Transcriptome profiling of a curdlan-producing Agrobacterium reveals conserved regulatory mechanisms of exopolysaccharide biosynthesis
Article Snippet: Purified RNA samples were stored at -80°C until analysis. .. The microarray is an 8 × 15 k custom DNA microarray from Agilent with probes designed using Agilent's eArray program.

Plasmid Preparation:

Article Title: Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds
Article Snippet: Custom DNA microarrays were obtained from Agilent Technologies (Waldbronn, Germany). .. Agilent's eArray platform was used to design oligonucleotide probes and assemble the custom 4-by-44,000 60-mer microarray.

Article Title: Agrobacterium tumefaciens ExoR Controls Acid Response Genes and Impacts Exopolysaccharide Synthesis, Horizontal Gene Transfer, and Virulence Gene Expression
Article Snippet: To identify all genes directly and indirectly affected by ExoR, we compared the transcriptome of wild-type C58 to a Δ exoR mutant using Agilent custom oligonucleotide microarrays. .. To identify all genes directly and indirectly affected by ExoR, we compared the transcriptome of wild-type C58 to a Δ exoR mutant using Agilent custom oligonucleotide microarrays.

Software:

Article Title: Transcriptome profiling of a curdlan-producing Agrobacterium reveals conserved regulatory mechanisms of exopolysaccharide biosynthesis
Article Snippet: The microarray is an 8 × 15 k custom DNA microarray from Agilent with probes designed using Agilent's eArray program. .. The microarray is an 8 × 15 k custom DNA microarray from Agilent with probes designed using Agilent's eArray program.

Article Title: Mechanisms of Resistance to Decitabine in the Myelodysplastic Syndrome
Article Snippet: Amplicons from patients with MDS after relapse were labeled with the Cy5 dye and cohybridized against amplicons from patients at diagnosis labeled with the Cy3 dye on Agilent Technologies 4×44 K custom DNA microarrays (Agilent, Santa Clara, CA) as described previously . .. Amplicons from patients with MDS after relapse were labeled with the Cy5 dye and cohybridized against amplicons from patients at diagnosis labeled with the Cy3 dye on Agilent Technologies 4×44 K custom DNA microarrays (Agilent, Santa Clara, CA) as described previously .

Article Title: Transcriptional Analysis of Lactobacillus brevis to N-Butanol and Ferulic Acid Stress Responses
Article Snippet: Cy3 and Cy5 (GE Healthcare) or Alexa Fluor (Invitrogen) dyes were used to label the cDNA samples. .. Custom cDNA microarrays (Agilent) containing 15,209 probes (excluding positive and negative controls) were designed using the software package Picky to maximize probe specificity and sensitivity under hybridization conditions with the following parameters. .. All probes are sixty base pair oligomers with 100% similarity to their corresponding target sequence.

RNA Extraction:

Article Title: Genomic and Genotoxic Responses to Controlled Weathered-Oil Exposures Confirm and Extend Field Studies on Impacts of the Deepwater Horizon Oil Spill on Native Killifish
Article Snippet: Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999). .. Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999).

Selection:

Article Title: High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes
Article Snippet: Oligonucleotide pools can be inexpensively synthesized from commercial sources (e.g., Atactic makes 4000 sequences for approximately $700) or even mechanically scoured from custom oligonucleotide microarray (e.g., Agilent microarray yields 240,000 sequences at a cost of $450). .. Oligonucleotide pools can be inexpensively synthesized from commercial sources (e.g., Atactic makes 4000 sequences for approximately $700) or even mechanically scoured from custom oligonucleotide microarray (e.g., Agilent microarray yields 240,000 sequences at a cost of $450).

Homogenization:

Article Title: Genomic and Genotoxic Responses to Controlled Weathered-Oil Exposures Confirm and Extend Field Studies on Impacts of the Deepwater Horizon Oil Spill on Native Killifish
Article Snippet: Gene expression responses were measured using custom oligonucleotide microarrays (Agilent eArray Design ID 027999). .. RNA extraction and microarray hybridizations followed the same methods as those reported in Whitehead et al. .

Immunoprecipitation:

Article Title: Smc5/6 Coordinates Formation and Resolution of Joint Molecules with Chromosome Morphology to Ensure Meiotic Divisions
Article Snippet: Briefly, Smc5 crosslinked chromatin was immunoprecipitated with 2 µl anti-myc 9E11 (Abcam) or 20 µl anti-V5 beads (Sigma-Aldrich). .. Immunoprecipitated and input DNA samples were cohybridized to a custom DNA microarray (Agilent) and data were normalized as previously described. .. The relative enrichment of Smc5 to Rec8 and Smc5 in spo11 versus SPO11 is the ratio of the values in each of the two datasets indicated.

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    Agilent technologies custom dna microarrays
    Transcript profiling using <t>DNA</t> <t>microarrays.</t>
    Custom Dna Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 84/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/custom dna microarrays/product/Agilent technologies
    Average 84 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    custom dna microarrays - by Bioz Stars, 2019-10
    84/100 stars
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    84
    Agilent technologies custom oligonucleotide high density european sea bass microarray
    Correlation between <t>microarray</t> and qPCR results. Fold change (FC) induction values of the different gene transcripts are plotted as log2 values of the relative fold change. The X-axis represent microarray data whereas the Y axis corresponds to qPCR data. The regression line and the corresponding r coefficient are also represented. For gene symbols and complete gene names see caption of Fig. 4
    Custom Oligonucleotide High Density European Sea Bass Microarray, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 84/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/custom oligonucleotide high density european sea bass microarray/product/Agilent technologies
    Average 84 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    custom oligonucleotide high density european sea bass microarray - by Bioz Stars, 2019-10
    84/100 stars
      Buy from Supplier

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    Transcript profiling using DNA microarrays.

    Journal:

    Article Title: Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds

    doi: 10.1128/JB.00154-13

    Figure Lengend Snippet: Transcript profiling using DNA microarrays.

    Article Snippet: Custom DNA microarrays were obtained from Agilent Technologies (Waldbronn, Germany).

    Techniques:

    Transcript profiling using DNA microarrays.

    Journal:

    Article Title: Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds

    doi: 10.1128/JB.00154-13

    Figure Lengend Snippet: Transcript profiling using DNA microarrays.

    Article Snippet: Custom DNA microarrays were obtained from Agilent Technologies (Waldbronn, Germany).

    Techniques:

    Transcript profiling using DNA microarrays.

    Journal:

    Article Title: Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds

    doi: 10.1128/JB.00154-13

    Figure Lengend Snippet: Transcript profiling using DNA microarrays.

    Article Snippet: Custom DNA microarrays were obtained from Agilent Technologies (Waldbronn, Germany).

    Techniques:

    Correlation between microarray and qPCR results. Fold change (FC) induction values of the different gene transcripts are plotted as log2 values of the relative fold change. The X-axis represent microarray data whereas the Y axis corresponds to qPCR data. The regression line and the corresponding r coefficient are also represented. For gene symbols and complete gene names see caption of Fig. 4

    Journal: BMC Genomics

    Article Title: Identification of conserved genes triggering puberty in European sea bass males (Dicentrarchus labrax) by microarray expression profiling

    doi: 10.1186/s12864-017-3823-2

    Figure Lengend Snippet: Correlation between microarray and qPCR results. Fold change (FC) induction values of the different gene transcripts are plotted as log2 values of the relative fold change. The X-axis represent microarray data whereas the Y axis corresponds to qPCR data. The regression line and the corresponding r coefficient are also represented. For gene symbols and complete gene names see caption of Fig. 4

    Article Snippet: Amplified samples (1.65 μg per sample) were hybridized to a custom oligonucleotide high-density European sea bass microarray (Agilent 4 × 44 K design format; http://www.agilent.com /) containing 60-mer oligonucleotides with a linker directly spotted on glass slides using the Agilent’s SurePrint Tecnology.

    Techniques: Microarray, Real-time Polymerase Chain Reaction, Flow Cytometry

    qPCR results for genes differentially expressed in the microarray during the onset of puberty in the European sea bass. Genes were selected according to their relevance in different reproductive events. a Genes involved in cell proliferation and cell cycle progression; proliferating cell nuclear antigen ( pcna ), centromere protein I ( cenpi ), spindle pole body component 25 ( spc25 ), centromere protein f ( cenpf ), thyroid hormone receptor interactor 13 ( trip13 ), and cdc28 protein kinase ( cdc28 ). b Genes involved in reproduction and growth; antimüllerian hormone ( amh ), aquaporin 1 ( aqp1 ), secretogranin II ( sgII ), agouti-related protein 2 ( agrp2 ), insulin-like growth factor binding protein 6 ( igfbp6 ). c Genes involved in the RA signalling pathway: RA-metabolizing enzyme cytochrome P450 26a1 ( cyp26a1 ), retinol binding protein 4 ( rbp4 ), RA-binding protein ( crabp1 ). This group also includes three RA-nuclear receptors, RA receptor alpha ( rarα ), retinoid X receptor alpha ( rxrα ), peroxisome proliferator-activated receptor gamma ( pparγ ) due to their relevance in this pathway. The stage-specific expression levels were normalized to those of the constitutively expressed 18S rRNA gene in each sample. Expression data are shown as mean normalized expression + SEM. Y-axis is represented in logarithmic scale for easier visualization. For each gene, bars on the left ( blue ) correspond to stage I testes and bars on the right ( red ) to stage II testes

    Journal: BMC Genomics

    Article Title: Identification of conserved genes triggering puberty in European sea bass males (Dicentrarchus labrax) by microarray expression profiling

    doi: 10.1186/s12864-017-3823-2

    Figure Lengend Snippet: qPCR results for genes differentially expressed in the microarray during the onset of puberty in the European sea bass. Genes were selected according to their relevance in different reproductive events. a Genes involved in cell proliferation and cell cycle progression; proliferating cell nuclear antigen ( pcna ), centromere protein I ( cenpi ), spindle pole body component 25 ( spc25 ), centromere protein f ( cenpf ), thyroid hormone receptor interactor 13 ( trip13 ), and cdc28 protein kinase ( cdc28 ). b Genes involved in reproduction and growth; antimüllerian hormone ( amh ), aquaporin 1 ( aqp1 ), secretogranin II ( sgII ), agouti-related protein 2 ( agrp2 ), insulin-like growth factor binding protein 6 ( igfbp6 ). c Genes involved in the RA signalling pathway: RA-metabolizing enzyme cytochrome P450 26a1 ( cyp26a1 ), retinol binding protein 4 ( rbp4 ), RA-binding protein ( crabp1 ). This group also includes three RA-nuclear receptors, RA receptor alpha ( rarα ), retinoid X receptor alpha ( rxrα ), peroxisome proliferator-activated receptor gamma ( pparγ ) due to their relevance in this pathway. The stage-specific expression levels were normalized to those of the constitutively expressed 18S rRNA gene in each sample. Expression data are shown as mean normalized expression + SEM. Y-axis is represented in logarithmic scale for easier visualization. For each gene, bars on the left ( blue ) correspond to stage I testes and bars on the right ( red ) to stage II testes

    Article Snippet: Amplified samples (1.65 μg per sample) were hybridized to a custom oligonucleotide high-density European sea bass microarray (Agilent 4 × 44 K design format; http://www.agilent.com /) containing 60-mer oligonucleotides with a linker directly spotted on glass slides using the Agilent’s SurePrint Tecnology.

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

    Structural details of copy number loss of 1.75-Mb 16q24 (A) or 1.85-Mb 22q13 (B) subtelomeric region resolved by high-density tiling microarray. A) The log2 ratio (y-axis) was plotted using the moving average along the genome position (x-axis). Representative early-onset T2DM data, from patients 1, 2, 3, and 4, respectively, are shown in Figures 2.1(a), 2.1(b), 2.1(c), and 2.1(d) . The black vertical bar shows the copy number plot along the genome. The two pale lines indicate the normal range of average log2 ratios for probes among normal individuals. Copy number losses are displayed as red vertical bars. “Copy number loss” was considered to be present when the downward-deviation of log2 ratios exceeded a threshold of 1SD from the median probe ratio. B) The log2 ratio (y-axis) was plotted using the moving average along the genome position (x-axis). Representative early-onset T2DM data from patients 1, 2, 3, and 4, respectively, are shown as Figures 2.2(a), 2.2(b), 2.2(c), and 2.2(d) . The black vertical bar shows the copy number plot along the genome. The two pale lines indicate the normal range of average log2 ratios for probes in normal individuals. Copy number losses are displayed as red vertical bars. “Copy number loss” was considered to be present when the downward-deviation of log2 ratios exceeded a threshold of 1SD from the median probe ratio.

    Journal: PLoS ONE

    Article Title: Simultaneous Copy Number Losses within Multiple Subtelomeric Regions in Early-Onset Type2 Diabetes Mellitus

    doi: 10.1371/journal.pone.0088602

    Figure Lengend Snippet: Structural details of copy number loss of 1.75-Mb 16q24 (A) or 1.85-Mb 22q13 (B) subtelomeric region resolved by high-density tiling microarray. A) The log2 ratio (y-axis) was plotted using the moving average along the genome position (x-axis). Representative early-onset T2DM data, from patients 1, 2, 3, and 4, respectively, are shown in Figures 2.1(a), 2.1(b), 2.1(c), and 2.1(d) . The black vertical bar shows the copy number plot along the genome. The two pale lines indicate the normal range of average log2 ratios for probes among normal individuals. Copy number losses are displayed as red vertical bars. “Copy number loss” was considered to be present when the downward-deviation of log2 ratios exceeded a threshold of 1SD from the median probe ratio. B) The log2 ratio (y-axis) was plotted using the moving average along the genome position (x-axis). Representative early-onset T2DM data from patients 1, 2, 3, and 4, respectively, are shown as Figures 2.2(a), 2.2(b), 2.2(c), and 2.2(d) . The black vertical bar shows the copy number plot along the genome. The two pale lines indicate the normal range of average log2 ratios for probes in normal individuals. Copy number losses are displayed as red vertical bars. “Copy number loss” was considered to be present when the downward-deviation of log2 ratios exceeded a threshold of 1SD from the median probe ratio.

    Article Snippet: We first screened CNVs in the whole genome using the deCODE-Illumina CNV370K BeadChip system which focuses on the CNV-rich region of the human genome, followed by validation and characterization using an Agilent region-targeted high-density custom-made oligonucleotide tiling microarray .

    Techniques: Microarray

    Extents of copy number losses within the 1.6-Mb 16q24 (A) and 4.8-Mb 22q13 (B) subtelomeric regions in early-onset T2DM patients as revealed by high-density oligonucleotide tiling microarray analysis. A) Dark horizontal bars represent the extents of copy number loss in each region in patients, as revealed by the Agilent custom tiling array analysis. Genome structures of the 10 patients subjects are aligned as horizontal bars from genome position 87,000,000 (left) to position 88,600,000 (right). Gray regions represent proximal ends of stretches where copy number status could not be inferred due to the presence of multiple low copy repeats. The upper map is an ideogram of chromosome 16 and the positions of putative genes in the 16q24 region described in the NCBI Map Viewer ( http://www.ncbi.nlm.nih.gov/projects/mapview ). Positions are given relative to NCBI Build 36 for chromosome 16. B) Dark horizontal bars represent the extent of copy number loss in each of the patients, as revealed by the Agilent custom tiling array analysis. Genome structures of the 12 patients subjects are aligned as horizontal bars from genome position 44,750,000 (left) to position 49,550,000 (right). Gray regions represent proximal ends of the stretch where copy number status could not be inferred due to the presence of multiple low copy repeats. The upper map is an ideogram of chromosome 22 and the positions of putative genes in the 22q13 region described in the NCBI Map Viewer ( http://www.ncbi.nlm.nih.gov/projects/mapview ). Positions are given relative to NCBI Build 36 for chromosome 22.

    Journal: PLoS ONE

    Article Title: Simultaneous Copy Number Losses within Multiple Subtelomeric Regions in Early-Onset Type2 Diabetes Mellitus

    doi: 10.1371/journal.pone.0088602

    Figure Lengend Snippet: Extents of copy number losses within the 1.6-Mb 16q24 (A) and 4.8-Mb 22q13 (B) subtelomeric regions in early-onset T2DM patients as revealed by high-density oligonucleotide tiling microarray analysis. A) Dark horizontal bars represent the extents of copy number loss in each region in patients, as revealed by the Agilent custom tiling array analysis. Genome structures of the 10 patients subjects are aligned as horizontal bars from genome position 87,000,000 (left) to position 88,600,000 (right). Gray regions represent proximal ends of stretches where copy number status could not be inferred due to the presence of multiple low copy repeats. The upper map is an ideogram of chromosome 16 and the positions of putative genes in the 16q24 region described in the NCBI Map Viewer ( http://www.ncbi.nlm.nih.gov/projects/mapview ). Positions are given relative to NCBI Build 36 for chromosome 16. B) Dark horizontal bars represent the extent of copy number loss in each of the patients, as revealed by the Agilent custom tiling array analysis. Genome structures of the 12 patients subjects are aligned as horizontal bars from genome position 44,750,000 (left) to position 49,550,000 (right). Gray regions represent proximal ends of the stretch where copy number status could not be inferred due to the presence of multiple low copy repeats. The upper map is an ideogram of chromosome 22 and the positions of putative genes in the 22q13 region described in the NCBI Map Viewer ( http://www.ncbi.nlm.nih.gov/projects/mapview ). Positions are given relative to NCBI Build 36 for chromosome 22.

    Article Snippet: We first screened CNVs in the whole genome using the deCODE-Illumina CNV370K BeadChip system which focuses on the CNV-rich region of the human genome, followed by validation and characterization using an Agilent region-targeted high-density custom-made oligonucleotide tiling microarray .

    Techniques: Microarray

    The extent of copy number losses within 1.3-Mb 4p16.3 subtelomeric region in 13 early-onset T2DM patients revealed by high-density oligonucleotide tiling microarray. Dark horizontal bars represent extent of copy number loss region in each patient revealed by Agilent custom tiling array. Genome structure of the 13 patients is aligned as horizontal bars from genome position 550,000 (left) to position 1,850,000 (right). Hatched region at position 1,423,147–1,478,646 represents genome gap-177 region. Gray regions represent proximal ends of stretch where copy number status was not inferred due to presence of multiple low copy repeats. Upper map shows ideogram of chromosome 4 and the positions of putative genes in 4p16.3 region described in Database of Genomic Variants ( http://projects.tcag.ca/variation/ ). Position is given relative to NCBI Build 35 for the chromosome 4.

    Journal: Experimental Diabetes Research

    Article Title: Frequent Loss of Genome Gap Region in 4p16.3 Subtelomere in Early-Onset Type 2 Diabetes Mellitus

    doi: 10.1155/2011/498460

    Figure Lengend Snippet: The extent of copy number losses within 1.3-Mb 4p16.3 subtelomeric region in 13 early-onset T2DM patients revealed by high-density oligonucleotide tiling microarray. Dark horizontal bars represent extent of copy number loss region in each patient revealed by Agilent custom tiling array. Genome structure of the 13 patients is aligned as horizontal bars from genome position 550,000 (left) to position 1,850,000 (right). Hatched region at position 1,423,147–1,478,646 represents genome gap-177 region. Gray regions represent proximal ends of stretch where copy number status was not inferred due to presence of multiple low copy repeats. Upper map shows ideogram of chromosome 4 and the positions of putative genes in 4p16.3 region described in Database of Genomic Variants ( http://projects.tcag.ca/variation/ ). Position is given relative to NCBI Build 35 for the chromosome 4.

    Article Snippet: In the search for susceptibility gene(s) for T2DM genes, we recruited a panel of 100 early-onset Japanese T2DM patients (onset age < 35 years) and 100 controls, and performed CNV analysis in the whole genome using the deCODE-Illumina CNV370K BeadChip which focuses on the CNV-rich region of the human genome, followed by validation and characterization using an Agilent region-targeted high-density custom-made oligonucleotide tiling microarray.

    Techniques: Microarray

    Detailed structure of copy number loss of 1.3-Mb 4p16.3 subtelomeric region resolved by high-density tiling microarray. Log 2 ratio ( y -axis) was plotted using moving average along the genome position ( x -axis). Four representative early-onset T2DM patients are shown as Figures 2(a) , 2(b) , 2(c) , and 2(d) , patient 1, 2, 3, and 4, respectively. For comparison, log 2 ratio of the region of two healthy normal individuals is also displayed as Figures 2(e) and 2(f) . Dark line represents copy number plot along the genome. Two light lines indicate normal range of average log 2 ratios for probes among normal individuals. Dotted line shows median of average log 2 ratio among normal individuals. Copy number losses are displayed as gray vertical bar. We defined two copy number classes, that is, “unchanged copy number” and “copy number loss.” “Unchanged copy number” was defined when the log 2 ratio stays within the mean ± 1 SD distribution among the normal population. “Copy number loss” was called when the downward-deviation of log 2 ratios exceeded a threshold of 1 SD from the median probe ratio.

    Journal: Experimental Diabetes Research

    Article Title: Frequent Loss of Genome Gap Region in 4p16.3 Subtelomere in Early-Onset Type 2 Diabetes Mellitus

    doi: 10.1155/2011/498460

    Figure Lengend Snippet: Detailed structure of copy number loss of 1.3-Mb 4p16.3 subtelomeric region resolved by high-density tiling microarray. Log 2 ratio ( y -axis) was plotted using moving average along the genome position ( x -axis). Four representative early-onset T2DM patients are shown as Figures 2(a) , 2(b) , 2(c) , and 2(d) , patient 1, 2, 3, and 4, respectively. For comparison, log 2 ratio of the region of two healthy normal individuals is also displayed as Figures 2(e) and 2(f) . Dark line represents copy number plot along the genome. Two light lines indicate normal range of average log 2 ratios for probes among normal individuals. Dotted line shows median of average log 2 ratio among normal individuals. Copy number losses are displayed as gray vertical bar. We defined two copy number classes, that is, “unchanged copy number” and “copy number loss.” “Unchanged copy number” was defined when the log 2 ratio stays within the mean ± 1 SD distribution among the normal population. “Copy number loss” was called when the downward-deviation of log 2 ratios exceeded a threshold of 1 SD from the median probe ratio.

    Article Snippet: In the search for susceptibility gene(s) for T2DM genes, we recruited a panel of 100 early-onset Japanese T2DM patients (onset age < 35 years) and 100 controls, and performed CNV analysis in the whole genome using the deCODE-Illumina CNV370K BeadChip which focuses on the CNV-rich region of the human genome, followed by validation and characterization using an Agilent region-targeted high-density custom-made oligonucleotide tiling microarray.

    Techniques: Microarray