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Agilent technologies g2565aa microarray scanner system
G2565aa Microarray Scanner System, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 92 stars, based on 16 article reviews
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g2565aa microarray scanner system - by Bioz Stars, 2020-03
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Related Articles

Clone Assay:

Article Title: Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis
Article Snippet: RNA was isolated from each sample and hybridized to a custom dual-dye gene expression microarray (Agilent) representing 20,226 transcripts identified via sequencing clones from stimulated vascular cells, literature review for genes important to cardiovascular function, and combination with a commercial clone set (Incyte). .. Arrays were scanned using Agilent’s G2565AA Microarray Scanner System, and Agilent feature extraction software was used to generate log2 ratios and P values for features on the array.

Article Title: Antagonistic Regulation of Cell-Matrix Adhesion by FosB and ?FosB/?2?FosB Encoded by Alternatively Spliced Forms of fosB Transcripts
Article Snippet: A mixture was made of 1 μg of each Cy3-labeled wild-type and Cy5-labeled mutant cDNA or each Cy3-labeled mutant and Cy5-labeled wild-type cDNA, and these cDNAs were then hybridized to Agilent Mouse cDNA Microarrays (G4104A, design file number: 000522R000679, Agilent Technologies) with 8500 unique clones from the Incyte mouse UniGene 1 clone set, according to the manufacturer's hybridization protocol. .. After washing, the microarray slides were analyzed with an Agilent G2565AA microarray scanner system.

Amplification:

Article Title: In Situ-Synthesized Novel Microarray Optimized for Mouse Stem Cell and Early Developmental Expression Profiling
Article Snippet: Fluorescent linear amplified cRNAs used in biological comparisons were hybridized to custom-made in situ synthesized 60-mer oligo microarrays containing 22,575 features including controls (Agilent Technologies), per the manufacturer's instructions. .. Hybridized microarrays were washed according to the manufacturer's protocol and scanned on an Agilent Technologies G2565AA Microarray Scanner System with SureScan technology.

Article Title: Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas
Article Snippet: Paragraph title: 2.5.1. RNA Amplification, Labeling, and Hybridization ... Finally, we have scanned the slides using an Agilent Technologies G2565AA Microarray Scanner system at a 5 µm resolution.

Article Title: Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Article Snippet: Paragraph title: RNA extraction, amplification, labeling and microarray hybridization ... Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system® at 5 μm resolution, using default parameters.

Article Title: Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
Article Snippet: Paragraph title: RNA Amplification, labeling and hybridization ... Finally, slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters.

Article Title: Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes
Article Snippet: Paragraph title: RNA amplification, labeling and hybridization ... Slides were then scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution.

Article Title: Antagonistic Regulation of Cell-Matrix Adhesion by FosB and ?FosB/?2?FosB Encoded by Alternatively Spliced Forms of fosB Transcripts
Article Snippet: For DNA microarray experiments, total RNA (10 μg) was labeled using an Agilent Linear Amplification/Labeling kit (Agilent Technologies, Wilmington, DE) according to the manufacturer's instructions. .. After washing, the microarray slides were analyzed with an Agilent G2565AA microarray scanner system.

Article Title: Transcriptomic Profiling of Gametogenesis in Triploid Pacific Oysters Crassostrea gigas: Towards an Understanding of Partial Sterility Associated with Triploidy
Article Snippet: cDNA microarray RNA amplification, labeling and one color hybridization were performed as previously described using the custom and validated design , and with the Low Input Quick Amp labeling kit (Agilent), Qiagen’s RNeasy mini spin columns and the Agilent Gene expression hybridization kit. .. Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution.

Article Title: Transcriptomic Analysis of Human Polarized Macrophages: More than One Role of Alternative Activation?
Article Snippet: The same amount of RNA from a commercially-available pool of human leucocyte total RNA (Clontech, Mountain View, CA, USA) was reversely transcribed, amplified and Cy3-labeled to be used as reference. .. Slides were scanned with an Agilent's G2565AA Microarray Scanner System.

Synthesized:

Article Title: In Situ-Synthesized Novel Microarray Optimized for Mouse Stem Cell and Early Developmental Expression Profiling
Article Snippet: Fluorescent linear amplified cRNAs used in biological comparisons were hybridized to custom-made in situ synthesized 60-mer oligo microarrays containing 22,575 features including controls (Agilent Technologies), per the manufacturer's instructions. .. Hybridized microarrays were washed according to the manufacturer's protocol and scanned on an Agilent Technologies G2565AA Microarray Scanner System with SureScan technology.

Microarray:

Article Title: In Situ-Synthesized Novel Microarray Optimized for Mouse Stem Cell and Early Developmental Expression Profiling
Article Snippet: .. Hybridized microarrays were washed according to the manufacturer's protocol and scanned on an Agilent Technologies G2565AA Microarray Scanner System with SureScan technology. .. Ratio data were extracted from scanned microarray images using Feature Extraction 5.1.1 software (Agilent Technologies), and dye-normalized, background-subtracted intensity and ratio data were exported to text and GEML-format files.

Article Title: Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas
Article Snippet: .. Finally, we have scanned the slides using an Agilent Technologies G2565AA Microarray Scanner system at a 5 µm resolution. ..

Article Title: Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Article Snippet: .. Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system® at 5 μm resolution, using default parameters. .. Features were extracted using the Agilent Feature Extraction software 6.1 (Agilent Technologies).

Article Title: miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors
Article Snippet: .. Processed slides were scanned with Agilent G2565AA Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA), with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 μm. ..

Article Title: Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis
Article Snippet: .. Arrays were scanned using Agilent’s G2565AA Microarray Scanner System, and Agilent feature extraction software was used to generate log2 ratios and P values for features on the array. ..

Article Title: Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
Article Snippet: .. Finally, slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters. .. Correction and Normalization Feature extraction and data normalization were conducted with Agilent Feature Extraction software 6.1. (Agilent Technologies), using the default/recommended normalization method.

Article Title: Physiological change under OsHV-1 contamination in Pacific oyster Crassostrea gigas through massive mortality events on fields
Article Snippet: .. The slides were then scanned on Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution. .. Analysis of each spot was made using Feature Extraction software 6.1 (Agilent Technologies), using the default/recommended parameters for the scanning, griding, extraction, correction and normalisation.

Article Title: Inflammatory Manifestations of Experimental Lymphatic InsufficiencyA New Mouse Model to Study Acquired Lymphedema
Article Snippet: .. Data Acquisition, Analysis, and Statistical Analysis Image acquisition of the mouse cDNA microarrays was performed on an Agilent G2565AA Microarray Scanner System. .. Feature extraction was performed with GenePix 4.0 software (Bucher Biotec, Basel, Switzerland).

Article Title: Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes
Article Snippet: .. Slides were then scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution. .. Correction and normalization Raw data extraction and normalization were conducted with Agilent Feature Extraction software 6.1 using the default/recommended normalization methods.

Article Title: Antagonistic Regulation of Cell-Matrix Adhesion by FosB and ?FosB/?2?FosB Encoded by Alternatively Spliced Forms of fosB Transcripts
Article Snippet: .. After washing, the microarray slides were analyzed with an Agilent G2565AA microarray scanner system. ..

Article Title: Transcriptomic Profiling of Gametogenesis in Triploid Pacific Oysters Crassostrea gigas: Towards an Understanding of Partial Sterility Associated with Triploidy
Article Snippet: .. Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution. ..

Article Title: Comparative transcriptomic analysis of Porphyromonas gingivalis biofilm and planktonic cells
Article Snippet: .. Image and data analysis The hybridized arrays were scanned using an Agilent G2565AA microarray scanner system (Agilent Technologies, Santa Clara, CA). .. Imagene 6.0 software (Biodiscovery, Los Angeles, CA) was used for spot finding, signal-background segmentation, and intensity quantification.

Article Title: Transcriptomic Analysis of Human Polarized Macrophages: More than One Role of Alternative Activation?
Article Snippet: .. Slides were scanned with an Agilent's G2565AA Microarray Scanner System. .. Dye-normalized, background-subtracted log-ratios of sample to reference expression were calculated using Agilent’s Feature Extraction Software version 9.5.

Article Title: Mycosis fungoides progression could be regulated by microRNAs
Article Snippet: .. Scanning was carried out immediately using the Agilent G2565AA Microarray Scanner System (Agilent Technologies) and data were collected with Feature Extraction v9.5 software (Agilent Technologies). .. Significant miRNAs (p < 0.05) were represented by a cluster using Babelomics 4.2 software ( http://babelomics.bioinfo.cipf.es ).

Article Title: Deregulated Expression of the Polycomb-Group Protein SUZ12 Target Genes Characterizes Mantle Cell Lymphoma
Article Snippet: .. Slides were scanned in an Agilent G2565AA microarray scanner system and data were extracted with feature extraction software (Agilent Technologies). .. To validate ChIP-on-chip results functionally in MCL tumoral samples, Pearson correlations between identified SUZ12 target genes and SUZ12 expression were calculated using the T-Rex program included in the Gene Expression Pattern Analysis Suite ( http://www.gepas.org /).

Incubation:

Article Title: miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors
Article Snippet: Labeling reaction was performed using 2 μl of CIP treated total RNA, 1.5 μl of Hy3 fluorescent dye, 2 μl DMSO and 2 μl of labeling enzyme, reaction was incubated at 16 °C for 1 h and heat inactivated by incubation at 65 °C for 15 min and left at 4 °C until hybridization step. .. Processed slides were scanned with Agilent G2565AA Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA), with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 μm.

Expressing:

Article Title: Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas
Article Snippet: Subsequently, gene expression wash buffer solution (5188–5327; Agilent Technologies), stabilization and drying solutions (5186–5979; Agilent Technologies) have been used to wash the slides. .. Finally, we have scanned the slides using an Agilent Technologies G2565AA Microarray Scanner system at a 5 µm resolution.

Article Title: Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Article Snippet: Samples were randomly hybridized onto 48 different slides, which were subsequently treated with Gene expression wash buffer solution® (5188–5327; Agilent Technologies), Stabilization and Drying solutions® (5185–5979; Agilent Technologies). .. Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system® at 5 μm resolution, using default parameters.

Article Title: Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis
Article Snippet: RNA was isolated from each sample and hybridized to a custom dual-dye gene expression microarray (Agilent) representing 20,226 transcripts identified via sequencing clones from stimulated vascular cells, literature review for genes important to cardiovascular function, and combination with a commercial clone set (Incyte). .. Arrays were scanned using Agilent’s G2565AA Microarray Scanner System, and Agilent feature extraction software was used to generate log2 ratios and P values for features on the array.

Article Title: Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
Article Snippet: Tissue samples were randomly hybridized onto 10 different slides, which were subsequently treated with Gene expression wash buffer solution (5188-5327; Agilent Technologies), and Stabilization and Drying solutions (5185-5979; Agilent Technologies). .. Finally, slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters.

Article Title: Physiological change under OsHV-1 contamination in Pacific oyster Crassostrea gigas through massive mortality events on fields
Article Snippet: After 16 hours at 60°C (Agilent oven with 10 rpm), slides were washed with the gene expression wash buffer solution (5188–5327; Agilent Technologies). .. The slides were then scanned on Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution.

Article Title: Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes
Article Snippet: Subsequently, slides were washed with Gene expression wash buffer solution (5188–5327; Agilent Technologies) and Stabilization and Drying solutions (5186–5979; Agilent Technologies). .. Slides were then scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution.

Article Title: Transcriptomic Profiling of Gametogenesis in Triploid Pacific Oysters Crassostrea gigas: Towards an Understanding of Partial Sterility Associated with Triploidy
Article Snippet: cDNA microarray RNA amplification, labeling and one color hybridization were performed as previously described using the custom and validated design , and with the Low Input Quick Amp labeling kit (Agilent), Qiagen’s RNeasy mini spin columns and the Agilent Gene expression hybridization kit. .. Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution.

Article Title: Transcriptomic Analysis of Human Polarized Macrophages: More than One Role of Alternative Activation?
Article Snippet: Paragraph title: Gene expression array ... Slides were scanned with an Agilent's G2565AA Microarray Scanner System.

Article Title: Mycosis fungoides progression could be regulated by microRNAs
Article Snippet: Scanning was carried out immediately using the Agilent G2565AA Microarray Scanner System (Agilent Technologies) and data were collected with Feature Extraction v9.5 software (Agilent Technologies). .. The microarray is available at the Gene Expression Omnibus under accession number GSE109421.

Article Title: Deregulated Expression of the Polycomb-Group Protein SUZ12 Target Genes Characterizes Mantle Cell Lymphoma
Article Snippet: Paragraph title: Gene Expression Profile ... Slides were scanned in an Agilent G2565AA microarray scanner system and data were extracted with feature extraction software (Agilent Technologies).

Modification:

Article Title: miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors
Article Snippet: Processed slides were scanned with Agilent G2565AA Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA), with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 μm. .. Fluorescence intensities on scanned images were quantified using Agilent Feature Extraction software version 9.5.3 (Agilent Technologies) using the modified Exiqon protocol and corresponding GAL files.

Transformation Assay:

Article Title: Comparative transcriptomic analysis of Porphyromonas gingivalis biofilm and planktonic cells
Article Snippet: Image and data analysis The hybridized arrays were scanned using an Agilent G2565AA microarray scanner system (Agilent Technologies, Santa Clara, CA). .. The intensity of each spot was local background corrected using GeneSight 4.1 (Biodiscovery) and the resultant data were log transformed such that the mean value for each channel (Cy3 and Cy5) had a log ratio of zero.

Hybridization:

Article Title: In Situ-Synthesized Novel Microarray Optimized for Mouse Stem Cell and Early Developmental Expression Profiling
Article Snippet: Paragraph title: Array Hybridization, Washing, and Scanning ... Hybridized microarrays were washed according to the manufacturer's protocol and scanned on an Agilent Technologies G2565AA Microarray Scanner System with SureScan technology.

Article Title: Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas
Article Snippet: Paragraph title: 2.5.1. RNA Amplification, Labeling, and Hybridization ... Finally, we have scanned the slides using an Agilent Technologies G2565AA Microarray Scanner system at a 5 µm resolution.

Article Title: Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Article Snippet: Paragraph title: RNA extraction, amplification, labeling and microarray hybridization ... Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system® at 5 μm resolution, using default parameters.

Article Title: miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors
Article Snippet: Paragraph title: Microarray hybridization ... Processed slides were scanned with Agilent G2565AA Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA), with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 μm.

Article Title: Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis
Article Snippet: Details of sample collection, RNA isolation, and microarray hybridization have been previously described ( ). .. Arrays were scanned using Agilent’s G2565AA Microarray Scanner System, and Agilent feature extraction software was used to generate log2 ratios and P values for features on the array.

Article Title: Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
Article Snippet: Paragraph title: RNA Amplification, labeling and hybridization ... Finally, slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters.

Article Title: Physiological change under OsHV-1 contamination in Pacific oyster Crassostrea gigas through massive mortality events on fields
Article Snippet: One thousand six hundred fifty nanograms of newly synthetized aRNA labelled with Cy3 were hybridized on the custom and validated 4x44K slide containing 31 918 EST [ , ] with the Gene Expression hybridization kit (5188–5242; Agilent Technologies) according to Agilent Technologies’ recommendations. .. The slides were then scanned on Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution.

Article Title: Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes
Article Snippet: Paragraph title: RNA amplification, labeling and hybridization ... Slides were then scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution.

Article Title: Antagonistic Regulation of Cell-Matrix Adhesion by FosB and ?FosB/?2?FosB Encoded by Alternatively Spliced Forms of fosB Transcripts
Article Snippet: A mixture was made of 1 μg of each Cy3-labeled wild-type and Cy5-labeled mutant cDNA or each Cy3-labeled mutant and Cy5-labeled wild-type cDNA, and these cDNAs were then hybridized to Agilent Mouse cDNA Microarrays (G4104A, design file number: 000522R000679, Agilent Technologies) with 8500 unique clones from the Incyte mouse UniGene 1 clone set, according to the manufacturer's hybridization protocol. .. After washing, the microarray slides were analyzed with an Agilent G2565AA microarray scanner system.

Article Title: Transcriptomic Profiling of Gametogenesis in Triploid Pacific Oysters Crassostrea gigas: Towards an Understanding of Partial Sterility Associated with Triploidy
Article Snippet: cDNA microarray RNA amplification, labeling and one color hybridization were performed as previously described using the custom and validated design , and with the Low Input Quick Amp labeling kit (Agilent), Qiagen’s RNeasy mini spin columns and the Agilent Gene expression hybridization kit. .. Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution.

Article Title: Transcriptomic Analysis of Human Polarized Macrophages: More than One Role of Alternative Activation?
Article Snippet: Slides were scanned with an Agilent's G2565AA Microarray Scanner System. .. Hybridization quality was checked using the software’s quality report.

Article Title: Mycosis fungoides progression could be regulated by microRNAs
Article Snippet: Paragraph title: Microarray procedures: miRNA hybridization ... Scanning was carried out immediately using the Agilent G2565AA Microarray Scanner System (Agilent Technologies) and data were collected with Feature Extraction v9.5 software (Agilent Technologies).

Dissection:

Article Title: Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis
Article Snippet: In brief, epicardial coronary arteries were harvested by dissection from explanted hearts of 22 human donors for orthotopic heart transplant. .. Arrays were scanned using Agilent’s G2565AA Microarray Scanner System, and Agilent feature extraction software was used to generate log2 ratios and P values for features on the array.

Sequencing:

Article Title: Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis
Article Snippet: RNA was isolated from each sample and hybridized to a custom dual-dye gene expression microarray (Agilent) representing 20,226 transcripts identified via sequencing clones from stimulated vascular cells, literature review for genes important to cardiovascular function, and combination with a commercial clone set (Incyte). .. Arrays were scanned using Agilent’s G2565AA Microarray Scanner System, and Agilent feature extraction software was used to generate log2 ratios and P values for features on the array.

Fluorescence:

Article Title: miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors
Article Snippet: Processed slides were scanned with Agilent G2565AA Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA), with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 μm. .. Fluorescence intensities on scanned images were quantified using Agilent Feature Extraction software version 9.5.3 (Agilent Technologies) using the modified Exiqon protocol and corresponding GAL files.

Mutagenesis:

Article Title: Antagonistic Regulation of Cell-Matrix Adhesion by FosB and ?FosB/?2?FosB Encoded by Alternatively Spliced Forms of fosB Transcripts
Article Snippet: A mixture was made of 1 μg of each Cy3-labeled wild-type and Cy5-labeled mutant cDNA or each Cy3-labeled mutant and Cy5-labeled wild-type cDNA, and these cDNAs were then hybridized to Agilent Mouse cDNA Microarrays (G4104A, design file number: 000522R000679, Agilent Technologies) with 8500 unique clones from the Incyte mouse UniGene 1 clone set, according to the manufacturer's hybridization protocol. .. After washing, the microarray slides were analyzed with an Agilent G2565AA microarray scanner system.

Isolation:

Article Title: Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis
Article Snippet: RNA was isolated from each sample and hybridized to a custom dual-dye gene expression microarray (Agilent) representing 20,226 transcripts identified via sequencing clones from stimulated vascular cells, literature review for genes important to cardiovascular function, and combination with a commercial clone set (Incyte). .. Arrays were scanned using Agilent’s G2565AA Microarray Scanner System, and Agilent feature extraction software was used to generate log2 ratios and P values for features on the array.

Labeling:

Article Title: In Situ-Synthesized Novel Microarray Optimized for Mouse Stem Cell and Early Developmental Expression Profiling
Article Snippet: Targets used to optimize reduced-input labeling protocols were hybridized to a 60-mer oligo microarray consisting of eight replicates of approximately 1000 probes that were evenly distributed across the detectable intensity range in previous experiments, with good signal-to-noise (data not shown). .. Hybridized microarrays were washed according to the manufacturer's protocol and scanned on an Agilent Technologies G2565AA Microarray Scanner System with SureScan technology.

Article Title: Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas
Article Snippet: Paragraph title: 2.5.1. RNA Amplification, Labeling, and Hybridization ... Finally, we have scanned the slides using an Agilent Technologies G2565AA Microarray Scanner system at a 5 µm resolution.

Article Title: Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Article Snippet: Paragraph title: RNA extraction, amplification, labeling and microarray hybridization ... Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system® at 5 μm resolution, using default parameters.

Article Title: miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors
Article Snippet: Labeled samples were subsequently loaded onto a miRNA microarray slide and hybridized over 16 h at 56 °C. .. Processed slides were scanned with Agilent G2565AA Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA), with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 μm.

Article Title: Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
Article Snippet: Paragraph title: RNA Amplification, labeling and hybridization ... Finally, slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters.

Article Title: Physiological change under OsHV-1 contamination in Pacific oyster Crassostrea gigas through massive mortality events on fields
Article Snippet: Dye incorporation and aRNA concentration were measured on the Nanodrop2000 spectrophotometer (Thermoscientific® ) and were congruent to the Agilent’s specifications after synthesis, a labeled aRNA concentration was superior to 2μg and an incorporation of Cy3 higher than 6 pmol Cy3 μg-1 aRNA. .. The slides were then scanned on Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution.

Article Title: Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes
Article Snippet: Paragraph title: RNA amplification, labeling and hybridization ... Slides were then scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution.

Article Title: Antagonistic Regulation of Cell-Matrix Adhesion by FosB and ?FosB/?2?FosB Encoded by Alternatively Spliced Forms of fosB Transcripts
Article Snippet: For DNA microarray experiments, total RNA (10 μg) was labeled using an Agilent Linear Amplification/Labeling kit (Agilent Technologies, Wilmington, DE) according to the manufacturer's instructions. .. After washing, the microarray slides were analyzed with an Agilent G2565AA microarray scanner system.

Article Title: Transcriptomic Profiling of Gametogenesis in Triploid Pacific Oysters Crassostrea gigas: Towards an Understanding of Partial Sterility Associated with Triploidy
Article Snippet: cDNA microarray RNA amplification, labeling and one color hybridization were performed as previously described using the custom and validated design , and with the Low Input Quick Amp labeling kit (Agilent), Qiagen’s RNeasy mini spin columns and the Agilent Gene expression hybridization kit. .. Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution.

Article Title: Transcriptomic Analysis of Human Polarized Macrophages: More than One Role of Alternative Activation?
Article Snippet: RNA references and samples were labeled separately and then hybridized together on 4X44 Whole Human Genome Agilent Microarray slides (Agilent Technologies). .. Slides were scanned with an Agilent's G2565AA Microarray Scanner System.

Article Title: Deregulated Expression of the Polycomb-Group Protein SUZ12 Target Genes Characterizes Mantle Cell Lymphoma
Article Snippet: 500 ng of RNA were labeled with cyanine 5-conjugated dUTP (Cy5) and hybridized onto the Agilent 44K whole genome microarray chip (Agilent Technologies) against a universal human reference RNA (Stratagene, La Jolla, CA) previously labeled with cyanine 3-conjugated dUTP (Cy3). .. Slides were scanned in an Agilent G2565AA microarray scanner system and data were extracted with feature extraction software (Agilent Technologies).

Purification:

Article Title: Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas
Article Snippet: Then, we have purified the amplified RNA (aRNA) samples using the Qiagen’s RNA easy mini spin columns (Venlo, Netherlands). .. Finally, we have scanned the slides using an Agilent Technologies G2565AA Microarray Scanner system at a 5 µm resolution.

Article Title: Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Article Snippet: After purification, RNA amplification and dye incorporation rates were verified using a ND-1000 spectrophotometer (Thermo Scientific) and shown to lie between 100 and 200 ng/μL (RNA concentration) and between 1 and 5 pmol/μL RNA (dye incorporation). .. Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system® at 5 μm resolution, using default parameters.

Article Title: Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
Article Snippet: After purification, aRNA amplification and dye incorporation rates were verified using a ND-1000 spectrophotometer (Nanodrop Technologies) and shown to lie between 200 and 500 ng/μL (aRNA concentration) and between 20 and 50 pmol/μg aRNA (dye incorporation). .. Finally, slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters.

Article Title: Physiological change under OsHV-1 contamination in Pacific oyster Crassostrea gigas through massive mortality events on fields
Article Snippet: Antisense RNA (aRNA) was purified on a column with the RNeasy® plus micro kit (Qiagen). .. The slides were then scanned on Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution.

Article Title: Antagonistic Regulation of Cell-Matrix Adhesion by FosB and ?FosB/?2?FosB Encoded by Alternatively Spliced Forms of fosB Transcripts
Article Snippet: Total RNA was purified from ES cells grown in the absence of feeder cells using ISOGEN (Nippon Gene, Tokyo, Japan), according to the manufacturer's instructions. .. After washing, the microarray slides were analyzed with an Agilent G2565AA microarray scanner system.

Chromatin Immunoprecipitation:

Article Title: Deregulated Expression of the Polycomb-Group Protein SUZ12 Target Genes Characterizes Mantle Cell Lymphoma
Article Snippet: 500 ng of RNA were labeled with cyanine 5-conjugated dUTP (Cy5) and hybridized onto the Agilent 44K whole genome microarray chip (Agilent Technologies) against a universal human reference RNA (Stratagene, La Jolla, CA) previously labeled with cyanine 3-conjugated dUTP (Cy3). .. Slides were scanned in an Agilent G2565AA microarray scanner system and data were extracted with feature extraction software (Agilent Technologies).

Software:

Article Title: Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Article Snippet: Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system® at 5 μm resolution, using default parameters. .. Features were extracted using the Agilent Feature Extraction software 6.1 (Agilent Technologies).

Article Title: miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors
Article Snippet: Processed slides were scanned with Agilent G2565AA Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA), with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 μm. .. Fluorescence intensities on scanned images were quantified using Agilent Feature Extraction software version 9.5.3 (Agilent Technologies) using the modified Exiqon protocol and corresponding GAL files.

Article Title: Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis
Article Snippet: .. Arrays were scanned using Agilent’s G2565AA Microarray Scanner System, and Agilent feature extraction software was used to generate log2 ratios and P values for features on the array. ..

Article Title: Physiological change under OsHV-1 contamination in Pacific oyster Crassostrea gigas through massive mortality events on fields
Article Snippet: The slides were then scanned on Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution. .. Analysis of each spot was made using Feature Extraction software 6.1 (Agilent Technologies), using the default/recommended parameters for the scanning, griding, extraction, correction and normalisation.

Article Title: Inflammatory Manifestations of Experimental Lymphatic InsufficiencyA New Mouse Model to Study Acquired Lymphedema
Article Snippet: Data Acquisition, Analysis, and Statistical Analysis Image acquisition of the mouse cDNA microarrays was performed on an Agilent G2565AA Microarray Scanner System. .. Feature extraction was performed with GenePix 4.0 software (Bucher Biotec, Basel, Switzerland).

Article Title: Antagonistic Regulation of Cell-Matrix Adhesion by FosB and ?FosB/?2?FosB Encoded by Alternatively Spliced Forms of fosB Transcripts
Article Snippet: After washing, the microarray slides were analyzed with an Agilent G2565AA microarray scanner system. .. Data analysis was performed using Agilent Feature Extraction software (Ver.

Article Title: Comparative transcriptomic analysis of Porphyromonas gingivalis biofilm and planktonic cells
Article Snippet: Image and data analysis The hybridized arrays were scanned using an Agilent G2565AA microarray scanner system (Agilent Technologies, Santa Clara, CA). .. Imagene 6.0 software (Biodiscovery, Los Angeles, CA) was used for spot finding, signal-background segmentation, and intensity quantification.

Article Title: Transcriptomic Analysis of Human Polarized Macrophages: More than One Role of Alternative Activation?
Article Snippet: Slides were scanned with an Agilent's G2565AA Microarray Scanner System. .. Dye-normalized, background-subtracted log-ratios of sample to reference expression were calculated using Agilent’s Feature Extraction Software version 9.5.

Article Title: Mycosis fungoides progression could be regulated by microRNAs
Article Snippet: .. Scanning was carried out immediately using the Agilent G2565AA Microarray Scanner System (Agilent Technologies) and data were collected with Feature Extraction v9.5 software (Agilent Technologies). .. Significant miRNAs (p < 0.05) were represented by a cluster using Babelomics 4.2 software ( http://babelomics.bioinfo.cipf.es ).

Article Title: Deregulated Expression of the Polycomb-Group Protein SUZ12 Target Genes Characterizes Mantle Cell Lymphoma
Article Snippet: .. Slides were scanned in an Agilent G2565AA microarray scanner system and data were extracted with feature extraction software (Agilent Technologies). .. To validate ChIP-on-chip results functionally in MCL tumoral samples, Pearson correlations between identified SUZ12 target genes and SUZ12 expression were calculated using the T-Rex program included in the Gene Expression Pattern Analysis Suite ( http://www.gepas.org /).

RNA Extraction:

Article Title: Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Article Snippet: Paragraph title: RNA extraction, amplification, labeling and microarray hybridization ... Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system® at 5 μm resolution, using default parameters.

In Situ:

Article Title: In Situ-Synthesized Novel Microarray Optimized for Mouse Stem Cell and Early Developmental Expression Profiling
Article Snippet: Fluorescent linear amplified cRNAs used in biological comparisons were hybridized to custom-made in situ synthesized 60-mer oligo microarrays containing 22,575 features including controls (Agilent Technologies), per the manufacturer's instructions. .. Hybridized microarrays were washed according to the manufacturer's protocol and scanned on an Agilent Technologies G2565AA Microarray Scanner System with SureScan technology.

Spectrophotometry:

Article Title: Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas
Article Snippet: The rates of dye incorporation and RNA amplification have been checked using an ND-1000 spectrophotometer (Nanodrop Technologies, Welmington, NC, USA). .. Finally, we have scanned the slides using an Agilent Technologies G2565AA Microarray Scanner system at a 5 µm resolution.

Article Title: Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Article Snippet: After purification, RNA amplification and dye incorporation rates were verified using a ND-1000 spectrophotometer (Thermo Scientific) and shown to lie between 100 and 200 ng/μL (RNA concentration) and between 1 and 5 pmol/μL RNA (dye incorporation). .. Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system® at 5 μm resolution, using default parameters.

Article Title: Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
Article Snippet: After purification, aRNA amplification and dye incorporation rates were verified using a ND-1000 spectrophotometer (Nanodrop Technologies) and shown to lie between 200 and 500 ng/μL (aRNA concentration) and between 20 and 50 pmol/μg aRNA (dye incorporation). .. Finally, slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters.

Article Title: Physiological change under OsHV-1 contamination in Pacific oyster Crassostrea gigas through massive mortality events on fields
Article Snippet: Dye incorporation and aRNA concentration were measured on the Nanodrop2000 spectrophotometer (Thermoscientific® ) and were congruent to the Agilent’s specifications after synthesis, a labeled aRNA concentration was superior to 2μg and an incorporation of Cy3 higher than 6 pmol Cy3 μg-1 aRNA. .. The slides were then scanned on Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution.

Article Title: Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes
Article Snippet: RNA amplification and dye incorporation rates were controlled using an ND-1000 spectrophotometer (Nanodrop Technologies). .. Slides were then scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 µm resolution.

Concentration Assay:

Article Title: Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas
Article Snippet: Afterwards, we measured the labeled aRNA concentration (between 200 and 500 ng/mL) and the dye incorporation (between 20 and 50 pmol/mg aRNA). .. Finally, we have scanned the slides using an Agilent Technologies G2565AA Microarray Scanner system at a 5 µm resolution.

Article Title: Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
Article Snippet: After purification, aRNA amplification and dye incorporation rates were verified using a ND-1000 spectrophotometer (Nanodrop Technologies) and shown to lie between 200 and 500 ng/μL (aRNA concentration) and between 20 and 50 pmol/μg aRNA (dye incorporation). .. Finally, slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters.

Article Title: Physiological change under OsHV-1 contamination in Pacific oyster Crassostrea gigas through massive mortality events on fields
Article Snippet: Dye incorporation and aRNA concentration were measured on the Nanodrop2000 spectrophotometer (Thermoscientific® ) and were congruent to the Agilent’s specifications after synthesis, a labeled aRNA concentration was superior to 2μg and an incorporation of Cy3 higher than 6 pmol Cy3 μg-1 aRNA. .. The slides were then scanned on Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution.

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    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
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    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
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    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
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    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