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Agilent technologies g2565ca scanner
G2565ca Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Related Articles

RNA Extraction:

Article Title: Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics
Article Snippet: Paragraph title: RNA extraction and hybridization on microarrays ... After hybridization of the cRNAs on the custom-designed ovine array, the chips were washed according to the manufacturer’s protocol and scanned using a G2565CA scanner (Agilent Technologies) at the resolution of 3 μm.

Amplification:

Article Title: Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics
Article Snippet: Each RNA sample (25 ng for sheep and 50 ng for pig) was amplified and cyanin 3 (Cy3) labeled, and subsequently the complementary RNA (cRNA) was checked for quality on a Nanodrop and on an Agilent 2100 Bioanalyzer. .. After hybridization of the cRNAs on the custom-designed ovine array, the chips were washed according to the manufacturer’s protocol and scanned using a G2565CA scanner (Agilent Technologies) at the resolution of 3 μm.

Article Title: Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression
Article Snippet: Experiments were performed following manufacturer’s instructions and the slides scanned on either a G2565BA or G2565CA scanner and analyzed using Agilent CGH Analytics software ver.5.0.14 or the Agilent Cytogenomics software 2.0.6.0 (Agilent Technologies Inc.). .. Duplication breakpoints were identified by PCR amplification with different combination of primers in each patient (Supp.

Sample Prep:

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: For sample preparation and array processing, the Agilent protocol “One-Color Microarray-Based Gene Expression Analysis” was used. .. Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters.

Expressing:

Article Title: Downregulation of miR-99a/let-7c/miR-125b miRNA cluster predicts clinical outcome in patients with unresected malignant pleural mesothelioma
Article Snippet: After washing, the slides were scanned by G2565CA scanner (Agilent Technologies) and data were extracted by Feature Extraction software v. 10 (Agilent Technologies). .. Microarray expression data were normalized using GeneSpring software v .12.6 (Agilent Technologies).

Article Title: Hierarchical differentiation competence in response to retinoic acid ensures stem cell maintenance during mouse spermatogenesis
Article Snippet: .. Microarray and quantitative (q) RT-PCR gene expression analyses Microarray analysis of transcripts from sorted fractions of spermatogonia was performed using a SurePrint G3 Mouse GE 8x60K Microarray Kit and G2505C or G2565CA scanner (Agilent Technologies). ..

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: Paragraph title: Gene Expression Microarray Analysis in Experiment 1 ... Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters.

Fluorescence:

Article Title: CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations
Article Snippet: Scanning of the microarrays was performed using a G2565CA scanner (Agilent). .. Data analysis was carried out with Agilent Technologies software, namely Feature Extraction for Cytogenomics V5.0 for the fluorescence ratio calculation and Agilent CytoGenomics 3.0.1.1 to visualize chromosomal imbalances.

Microarray:

Article Title: Downregulation of miR-99a/let-7c/miR-125b miRNA cluster predicts clinical outcome in patients with unresected malignant pleural mesothelioma
Article Snippet: Paragraph title: Microarray analysis ... After washing, the slides were scanned by G2565CA scanner (Agilent Technologies) and data were extracted by Feature Extraction software v. 10 (Agilent Technologies).

Article Title: Lack of Major Genome Instability in Tumors of p53 Null Rats
Article Snippet: Microarrays were scanned with a G2565CA scanner (Agilent, Santa Clara, CA, USA) at resolution 2 μm, double pass. .. Microarray slides were reused once by removing the hybridized probe from the slide (after image acquisition) using the NimbleGen Array Reuse Kit (Roche Nimblegen, Basel, Switzerland).

Article Title: Hierarchical differentiation competence in response to retinoic acid ensures stem cell maintenance during mouse spermatogenesis
Article Snippet: .. Microarray and quantitative (q) RT-PCR gene expression analyses Microarray analysis of transcripts from sorted fractions of spermatogonia was performed using a SurePrint G3 Mouse GE 8x60K Microarray Kit and G2505C or G2565CA scanner (Agilent Technologies). ..

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: Paragraph title: Gene Expression Microarray Analysis in Experiment 1 ... Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters.

Software:

Article Title: Downregulation of miR-99a/let-7c/miR-125b miRNA cluster predicts clinical outcome in patients with unresected malignant pleural mesothelioma
Article Snippet: .. After washing, the slides were scanned by G2565CA scanner (Agilent Technologies) and data were extracted by Feature Extraction software v. 10 (Agilent Technologies). .. Microarray expression data were normalized using GeneSpring software v .12.6 (Agilent Technologies).

Article Title: Phylogeny and Population Structure of Brown Rot- and Moko Disease-Causing Strains of Ralstonia solanacearum Phylotype II
Article Snippet: .. Slides were scanned at a 5-μm resolution using the G2565CA scanner managed by Scan Control software, version 8.5 (Agilent Technologies). .. Data were extracted from the 16-bit tagged-image format file (TIFF) image with Feature Extraction software, version 10.5.1.1 (Agilent Technologies).

Article Title: Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics
Article Snippet: In brief, the commercial probes with poor Sigreannot scores ( ) were replaced with new probes designed using the e-array software from Agilent Technologies and including ovine or porcine orthologs of genes known to be selectively expressed in human and mouse DC subsets ( ). .. After hybridization of the cRNAs on the custom-designed ovine array, the chips were washed according to the manufacturer’s protocol and scanned using a G2565CA scanner (Agilent Technologies) at the resolution of 3 μm.

Article Title: CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations
Article Snippet: Scanning of the microarrays was performed using a G2565CA scanner (Agilent). .. Data analysis was carried out with Agilent Technologies software, namely Feature Extraction for Cytogenomics V5.0 for the fluorescence ratio calculation and Agilent CytoGenomics 3.0.1.1 to visualize chromosomal imbalances.

Article Title: Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression
Article Snippet: .. Experiments were performed following manufacturer’s instructions and the slides scanned on either a G2565BA or G2565CA scanner and analyzed using Agilent CGH Analytics software ver.5.0.14 or the Agilent Cytogenomics software 2.0.6.0 (Agilent Technologies Inc.). .. Duplication breakpoints were identified by PCR amplification with different combination of primers in each patient (Supp.

Article Title: Lack of Major Genome Instability in Tumors of p53 Null Rats
Article Snippet: Microarrays were scanned with a G2565CA scanner (Agilent, Santa Clara, CA, USA) at resolution 2 μm, double pass. .. Image analysis was performed using Feature extraction software version 10.5.1.1 (Roche Nimblegen) and CGH-segMNT in NimbleScan 2.6 software (Roche NimbleGen).

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: .. Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters. .. Microarray data analyses were performed using GeneSpring GX software version 14.5 (Agilent Technologies).

Labeling:

Article Title: Downregulation of miR-99a/let-7c/miR-125b miRNA cluster predicts clinical outcome in patients with unresected malignant pleural mesothelioma
Article Snippet: Briefly, 100 ng of total RNA and an appropriate dilution of Spike-in controls underwent dephosphorylation and labeling step with Cy3CTP and purification using Micro Bio-Spin™ P-6 Gel Columns (Bio-Rad, Hercules, CA, USA). .. After washing, the slides were scanned by G2565CA scanner (Agilent Technologies) and data were extracted by Feature Extraction software v. 10 (Agilent Technologies).

Article Title: Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics
Article Snippet: Each RNA sample (25 ng for sheep and 50 ng for pig) was amplified and cyanin 3 (Cy3) labeled, and subsequently the complementary RNA (cRNA) was checked for quality on a Nanodrop and on an Agilent 2100 Bioanalyzer. .. After hybridization of the cRNAs on the custom-designed ovine array, the chips were washed according to the manufacturer’s protocol and scanned using a G2565CA scanner (Agilent Technologies) at the resolution of 3 μm.

Article Title: CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations
Article Snippet: DNA was labeled (cyanine 3 or cyanine 5) using the Genomic DNA ULS Labeling Kit from Agilent Technologies and hybridized onto the microarrays according to the manufacturer’s instructions (Agilent). .. Scanning of the microarrays was performed using a G2565CA scanner (Agilent).

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: Thereafter, Cy3-labeled cRNA was produced using the Agilent Low Input Quick Amp Labeling (1-color), purified with the RNeasy Mini Kit, fragmented using the In Situ Hybridization Kit (Agilent Technologies), and subjected to hybridization by incubation in a hybridization oven (Agilent Technologies). .. Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters.

Mouse Assay:

Article Title: Hierarchical differentiation competence in response to retinoic acid ensures stem cell maintenance during mouse spermatogenesis
Article Snippet: Microarray and quantitative (q) RT-PCR gene expression analyses Microarray analysis of transcripts from sorted fractions of spermatogonia was performed using a SurePrint G3 Mouse GE 8x60K Microarray Kit and G2505C or G2565CA scanner (Agilent Technologies). .. For GFRα1+ and KIT+ fractions, each sample was collected from a single individual; samples from two mice were pooled to analyze NGN3+ cells.

Produced:

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: Thereafter, Cy3-labeled cRNA was produced using the Agilent Low Input Quick Amp Labeling (1-color), purified with the RNeasy Mini Kit, fragmented using the In Situ Hybridization Kit (Agilent Technologies), and subjected to hybridization by incubation in a hybridization oven (Agilent Technologies). .. Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Hierarchical differentiation competence in response to retinoic acid ensures stem cell maintenance during mouse spermatogenesis
Article Snippet: .. Microarray and quantitative (q) RT-PCR gene expression analyses Microarray analysis of transcripts from sorted fractions of spermatogonia was performed using a SurePrint G3 Mouse GE 8x60K Microarray Kit and G2505C or G2565CA scanner (Agilent Technologies). ..

Incubation:

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: Thereafter, Cy3-labeled cRNA was produced using the Agilent Low Input Quick Amp Labeling (1-color), purified with the RNeasy Mini Kit, fragmented using the In Situ Hybridization Kit (Agilent Technologies), and subjected to hybridization by incubation in a hybridization oven (Agilent Technologies). .. Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters.

Polymerase Chain Reaction:

Article Title: Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression
Article Snippet: Experiments were performed following manufacturer’s instructions and the slides scanned on either a G2565BA or G2565CA scanner and analyzed using Agilent CGH Analytics software ver.5.0.14 or the Agilent Cytogenomics software 2.0.6.0 (Agilent Technologies Inc.). .. Duplication breakpoints were identified by PCR amplification with different combination of primers in each patient (Supp.

De-Phosphorylation Assay:

Article Title: Downregulation of miR-99a/let-7c/miR-125b miRNA cluster predicts clinical outcome in patients with unresected malignant pleural mesothelioma
Article Snippet: Briefly, 100 ng of total RNA and an appropriate dilution of Spike-in controls underwent dephosphorylation and labeling step with Cy3CTP and purification using Micro Bio-Spin™ P-6 Gel Columns (Bio-Rad, Hercules, CA, USA). .. After washing, the slides were scanned by G2565CA scanner (Agilent Technologies) and data were extracted by Feature Extraction software v. 10 (Agilent Technologies).

DNA Labeling:

Article Title: Lack of Major Genome Instability in Tumors of p53 Null Rats
Article Snippet: The oligonucleotide design, array fabrication, DNA labeling, hybridization were performed according to manufacturer’s instructions. .. Microarrays were scanned with a G2565CA scanner (Agilent, Santa Clara, CA, USA) at resolution 2 μm, double pass.

Sequencing:

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: Gene Expression Microarray Analysis in Experiment 1 Gene expression analysis was conducted using Agilent Rat Oligo arrays with approximately 60 000 probes for known genes and expressed sequence tags (Agilent Technologies). .. Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters.

Purification:

Article Title: Downregulation of miR-99a/let-7c/miR-125b miRNA cluster predicts clinical outcome in patients with unresected malignant pleural mesothelioma
Article Snippet: Briefly, 100 ng of total RNA and an appropriate dilution of Spike-in controls underwent dephosphorylation and labeling step with Cy3CTP and purification using Micro Bio-Spin™ P-6 Gel Columns (Bio-Rad, Hercules, CA, USA). .. After washing, the slides were scanned by G2565CA scanner (Agilent Technologies) and data were extracted by Feature Extraction software v. 10 (Agilent Technologies).

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: Thereafter, Cy3-labeled cRNA was produced using the Agilent Low Input Quick Amp Labeling (1-color), purified with the RNeasy Mini Kit, fragmented using the In Situ Hybridization Kit (Agilent Technologies), and subjected to hybridization by incubation in a hybridization oven (Agilent Technologies). .. Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters.

In Situ Hybridization:

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: Thereafter, Cy3-labeled cRNA was produced using the Agilent Low Input Quick Amp Labeling (1-color), purified with the RNeasy Mini Kit, fragmented using the In Situ Hybridization Kit (Agilent Technologies), and subjected to hybridization by incubation in a hybridization oven (Agilent Technologies). .. Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters.

Hybridization:

Article Title: Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics
Article Snippet: .. After hybridization of the cRNAs on the custom-designed ovine array, the chips were washed according to the manufacturer’s protocol and scanned using a G2565CA scanner (Agilent Technologies) at the resolution of 3 μm. .. The resulting .tiff images were extracted using the Feature Extraction software v10.7.3.1 (Agilent Technologies), using the GE1_107_Sep09 protocol.

Article Title: Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression
Article Snippet: Paragraph title: Custom Array Comparative Genomic Hybridization and Breakpoint Identification ... Experiments were performed following manufacturer’s instructions and the slides scanned on either a G2565BA or G2565CA scanner and analyzed using Agilent CGH Analytics software ver.5.0.14 or the Agilent Cytogenomics software 2.0.6.0 (Agilent Technologies Inc.).

Article Title: Lack of Major Genome Instability in Tumors of p53 Null Rats
Article Snippet: Paragraph title: Array Comparative Genomic Hybridization ... Microarrays were scanned with a G2565CA scanner (Agilent, Santa Clara, CA, USA) at resolution 2 μm, double pass.

Article Title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Nongenotoxic Hepatocarcinogens
Article Snippet: Thereafter, Cy3-labeled cRNA was produced using the Agilent Low Input Quick Amp Labeling (1-color), purified with the RNeasy Mini Kit, fragmented using the In Situ Hybridization Kit (Agilent Technologies), and subjected to hybridization by incubation in a hybridization oven (Agilent Technologies). .. Hybridized slides were scanned (G2565CA scanner, Agilent Technologies), and data were obtained using Agilent Feature Extraction software version 11.7.1.1 with defaults for all parameters.

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  • 99
    Agilent technologies dna microarray scanner
    Effects of CNT-1 and CNT-2 on gene expression in NR8383 cells. Venn diagram showing the number of upregulated and downregulated genes in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h (A). Heat map generated from <t>DNA</t> <t>microarray</t> data reflecting differential expression of genes involved in the response to stimulus (GO: 0050896) in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h. Expression levels are colored blue for low intensity and red for high intensity (see scale at the bottom right corner) (B).
    Dna Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 1473 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna microarray scanner/product/Agilent technologies
    Average 99 stars, based on 1473 article reviews
    Price from $9.99 to $1999.99
    dna microarray scanner - by Bioz Stars, 2020-03
    99/100 stars
      Buy from Supplier

    99
    Agilent technologies microarray scanner
    Distinct effects by aging and RSV on gene expression. Panel A shows each individual animal in a principal component analysis (PCA) of the <t>microarray</t> data of lung samples derived at day 0 (mock-inoculated, black, n = 4/group), or at day 2 (red, n = 5/group) or day 5 (green, n = 5/group) after inoculation with RSV. Aging-regulated expression appears by PC1, RSV-regulated gene expression appears along PC2. Y, young (circles); O, old (triangles); M, mock control; R, RSV-inoculated. Panel B shows a Venn-diagram depicting numbers of genes that are significantly upregulated (↑), downregulated (↓), or show no significant response (−). The three symbols indicate from left to right: response to RSV in young mice, response to RSV in old mice, response to aging, respectively.
    Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 105 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/microarray scanner/product/Agilent technologies
    Average 99 stars, based on 105 article reviews
    Price from $9.99 to $1999.99
    microarray scanner - by Bioz Stars, 2020-03
    99/100 stars
      Buy from Supplier

    99
    Agilent technologies g2565ca dna microarray scanner
    Chromosome aneuploidy in L. infantum Sb2000.1 and Sb4000.4 antimony-resistant mutants. Log 2 -transformed Sb2000.1/WT expression ratios of the upregulated chromosome 1 ( A ), chromosome 11 ( B ) and chromosome 25 ( C ) and of the downregulated chromosome 9 ( D ), chromosome 12 ( E ) and chromosome 32 ( F ) plotted as a function of the location of <t>microarray</t> probes on each chromosomes. For each plot, the log 2 -transformed gene expression ratios of chromosome 30, which was equally expressed in both samples, are shown as a control (grey line). Quantitative Southern blot hybridizations of digested genomic <t>DNA</t> extracted from L. infantum WT (lane 1), Sb2000.1 (lane 2) and Sb4000.4 (lane 3) were performed to correlate gene expression modulation of entire chromosomes with the chromosome DNA copy number. The hybridization signal of LinJ30_V3.2990 was used for normalization. The hybridization signals were quantified using ImageQuant 5.2 (Molecular Dynamics) and the fold differences in DNA copy number of Sb2000.1 compared to WT are found below each blot.
    G2565ca Dna Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/g2565ca dna microarray scanner/product/Agilent technologies
    Average 99 stars, based on 16 article reviews
    Price from $9.99 to $1999.99
    g2565ca dna microarray scanner - by Bioz Stars, 2020-03
    99/100 stars
      Buy from Supplier

    Image Search Results


    Effects of CNT-1 and CNT-2 on gene expression in NR8383 cells. Venn diagram showing the number of upregulated and downregulated genes in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h (A). Heat map generated from DNA microarray data reflecting differential expression of genes involved in the response to stimulus (GO: 0050896) in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h. Expression levels are colored blue for low intensity and red for high intensity (see scale at the bottom right corner) (B).

    Journal: Inhalation Toxicology

    Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity

    doi: 10.3109/08958378.2015.1026620

    Figure Lengend Snippet: Effects of CNT-1 and CNT-2 on gene expression in NR8383 cells. Venn diagram showing the number of upregulated and downregulated genes in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h (A). Heat map generated from DNA microarray data reflecting differential expression of genes involved in the response to stimulus (GO: 0050896) in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h. Expression levels are colored blue for low intensity and red for high intensity (see scale at the bottom right corner) (B).

    Article Snippet: Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution.

    Techniques: Expressing, Generated, Microarray

    Distinct effects by aging and RSV on gene expression. Panel A shows each individual animal in a principal component analysis (PCA) of the microarray data of lung samples derived at day 0 (mock-inoculated, black, n = 4/group), or at day 2 (red, n = 5/group) or day 5 (green, n = 5/group) after inoculation with RSV. Aging-regulated expression appears by PC1, RSV-regulated gene expression appears along PC2. Y, young (circles); O, old (triangles); M, mock control; R, RSV-inoculated. Panel B shows a Venn-diagram depicting numbers of genes that are significantly upregulated (↑), downregulated (↓), or show no significant response (−). The three symbols indicate from left to right: response to RSV in young mice, response to RSV in old mice, response to aging, respectively.

    Journal: Scientific Reports

    Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance

    doi: 10.1038/s41598-018-35180-2

    Figure Lengend Snippet: Distinct effects by aging and RSV on gene expression. Panel A shows each individual animal in a principal component analysis (PCA) of the microarray data of lung samples derived at day 0 (mock-inoculated, black, n = 4/group), or at day 2 (red, n = 5/group) or day 5 (green, n = 5/group) after inoculation with RSV. Aging-regulated expression appears by PC1, RSV-regulated gene expression appears along PC2. Y, young (circles); O, old (triangles); M, mock control; R, RSV-inoculated. Panel B shows a Venn-diagram depicting numbers of genes that are significantly upregulated (↑), downregulated (↓), or show no significant response (−). The three symbols indicate from left to right: response to RSV in young mice, response to RSV in old mice, response to aging, respectively.

    Article Snippet: After washing (NimbleGen Arrays User’s Guide – Gene Expression Arrays Version 5.0), slides were scanned in an ozone-free room with a microarray scanner (Agilent DNA microarray scanner G2565CA, Agilent Technologies).

    Techniques: Expressing, Microarray, Derivative Assay, Mouse Assay

    Principle of multiplex SOMAmer affinity assay. (A) Binding. SOMAmers and samples are mixed in 96-well microwell plates and allowed to bind. Cognate and non-cognate SOMAmer-target protein complexes form. Free SOMAmer and protein are also present. (B–H) Schematic sequence of assay steps leading to quantitative readout of target proteins. (B) SOMAmer-protein binding: DNA-based SOMAmer molecules (gold, blue, and green) have unique shapes selected to bind to a specific protein. SOMAmers contain biotin (B), a photo-cleavable linker (L) and a fluorescent tag at the 5′ end. Most SOMAmers (gold and green) bind to cognate proteins (red), but some (blue) form non-cognate complexes. (C) Catch-1. SOMAmers are captured onto a bead coated with streptavidin (SA) which binds biotin. Un-complexed proteins are washed away. (D) Proteins are tagged with NHS-biotin. (E) Photocleavage and kinetic challenge. UV light (hν) cleaves the linker and SOMAmers are released from beads, leaving biotin on bead. Samples are challenged with anionic competitor (dextran sulfate). Non-cognate complexes (blue SOMAmer) preferentially dissociate. (F) Catch-2 SOMAmer-protein complexes are captured onto new avidin coated beads by protein biotin tag. Free SOMAmers are washed away. (G) SOMAmers are released from complexes into solution at high pH. (H) Remaining SOMAmers are quantified by hybridization to microarray containing single-stranded DNA probes complementary to SOMAmer DNA sequence, which form a double-stranded helix. Hybridized SOMAmers are detected by fluorescent tags when the array is scanned.

    Journal: PLoS ONE

    Article Title: Aptamer-Based Multiplexed Proteomic Technology for Biomarker DiscoveryUnlocking Biomarker Discovery: Large Scale Application of Aptamer Proteomic Technology for Early Detection of Lung Cancer

    doi: 10.1371/journal.pone.0015004

    Figure Lengend Snippet: Principle of multiplex SOMAmer affinity assay. (A) Binding. SOMAmers and samples are mixed in 96-well microwell plates and allowed to bind. Cognate and non-cognate SOMAmer-target protein complexes form. Free SOMAmer and protein are also present. (B–H) Schematic sequence of assay steps leading to quantitative readout of target proteins. (B) SOMAmer-protein binding: DNA-based SOMAmer molecules (gold, blue, and green) have unique shapes selected to bind to a specific protein. SOMAmers contain biotin (B), a photo-cleavable linker (L) and a fluorescent tag at the 5′ end. Most SOMAmers (gold and green) bind to cognate proteins (red), but some (blue) form non-cognate complexes. (C) Catch-1. SOMAmers are captured onto a bead coated with streptavidin (SA) which binds biotin. Un-complexed proteins are washed away. (D) Proteins are tagged with NHS-biotin. (E) Photocleavage and kinetic challenge. UV light (hν) cleaves the linker and SOMAmers are released from beads, leaving biotin on bead. Samples are challenged with anionic competitor (dextran sulfate). Non-cognate complexes (blue SOMAmer) preferentially dissociate. (F) Catch-2 SOMAmer-protein complexes are captured onto new avidin coated beads by protein biotin tag. Free SOMAmers are washed away. (G) SOMAmers are released from complexes into solution at high pH. (H) Remaining SOMAmers are quantified by hybridization to microarray containing single-stranded DNA probes complementary to SOMAmer DNA sequence, which form a double-stranded helix. Hybridized SOMAmers are detected by fluorescent tags when the array is scanned.

    Article Snippet: Microarray Imaging The microarray slides were imaged with a microarray scanner (Agilent G2565CA Microarray Scanner System, Agilent Technologies) in the Cy3-channel at 5 µm resolution at 100% PMT setting and the XRD option enabled at 0.05.

    Techniques: Multiplex Assay, Binding Assay, Sequencing, Protein Binding, Avidin-Biotin Assay, Hybridization, Microarray

    Chromosome aneuploidy in L. infantum Sb2000.1 and Sb4000.4 antimony-resistant mutants. Log 2 -transformed Sb2000.1/WT expression ratios of the upregulated chromosome 1 ( A ), chromosome 11 ( B ) and chromosome 25 ( C ) and of the downregulated chromosome 9 ( D ), chromosome 12 ( E ) and chromosome 32 ( F ) plotted as a function of the location of microarray probes on each chromosomes. For each plot, the log 2 -transformed gene expression ratios of chromosome 30, which was equally expressed in both samples, are shown as a control (grey line). Quantitative Southern blot hybridizations of digested genomic DNA extracted from L. infantum WT (lane 1), Sb2000.1 (lane 2) and Sb4000.4 (lane 3) were performed to correlate gene expression modulation of entire chromosomes with the chromosome DNA copy number. The hybridization signal of LinJ30_V3.2990 was used for normalization. The hybridization signals were quantified using ImageQuant 5.2 (Molecular Dynamics) and the fold differences in DNA copy number of Sb2000.1 compared to WT are found below each blot.

    Journal: Nucleic Acids Research

    Article Title: Gene expression modulation is associated with gene amplification, supernumerary chromosomes and chromosome loss in antimony-resistant Leishmania infantum

    doi: 10.1093/nar/gkn1069

    Figure Lengend Snippet: Chromosome aneuploidy in L. infantum Sb2000.1 and Sb4000.4 antimony-resistant mutants. Log 2 -transformed Sb2000.1/WT expression ratios of the upregulated chromosome 1 ( A ), chromosome 11 ( B ) and chromosome 25 ( C ) and of the downregulated chromosome 9 ( D ), chromosome 12 ( E ) and chromosome 32 ( F ) plotted as a function of the location of microarray probes on each chromosomes. For each plot, the log 2 -transformed gene expression ratios of chromosome 30, which was equally expressed in both samples, are shown as a control (grey line). Quantitative Southern blot hybridizations of digested genomic DNA extracted from L. infantum WT (lane 1), Sb2000.1 (lane 2) and Sb4000.4 (lane 3) were performed to correlate gene expression modulation of entire chromosomes with the chromosome DNA copy number. The hybridization signal of LinJ30_V3.2990 was used for normalization. The hybridization signals were quantified using ImageQuant 5.2 (Molecular Dynamics) and the fold differences in DNA copy number of Sb2000.1 compared to WT are found below each blot.

    Article Snippet: Microarray data acquisition and analysis Detection of the Alexa Fluor 555 and Alexa Fluor 647 signals was performed on a G2565CA DNA microarray scanner (Agilent technologies) at a 5-μm resolution.

    Techniques: Transformation Assay, Expressing, Microarray, Southern Blot, Hybridization