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Agilent technologies g2565ca microarray scanner
G2565ca Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 101 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Related Articles

Indirect Immunoperoxidase Assay:

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Article Snippet: The signals were captured by a Microarray Scanner (G2565, Agilent Technologies, Santa Clara, USA). .. The generated data was analysed using the software Genespring 12.1 (Agilent Technologies) and Ingenuity Pathway Analysis (IPA; Qiagen).

Centrifugation:

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: .. Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software. ..

Amplification:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturer's protocol (Agilent). .. Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent).

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance
Article Snippet: The yields of amplified RNA and incorporation of CyDye were determined by using a NanoDrop spectrophotometer. .. 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).

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The cDNA was transcribed and amplified with T7 RNA polymerase to produce the cRNA labeled with cyanine 3. .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Article Title: Redox-dependent condensation of the mycobacterial nucleoid by WhiB4
Article Snippet: RNA amplification, cDNA labeling, microarray hybridization, scanning, and data analysis were performed at the UDSCMAC as described previously . .. Slides were scanned on a microarray scanner (Agilent Technologies) and analyzed using the GeneSpring software.

Article Title: ?9-Tetrahydrocannabinol Disrupts Estrogen-Signaling through Up-Regulation of Estrogen Receptor β (ERβ)
Article Snippet: From both cells, total RNA was extracted, and cDNA synthesizing and cRNA labeling were conducted using a Low RNA Fluorescent Linear Amplification kit (Agilent, Palo Alto, CA, USA). .. Specific hybridization was analyzed using a Microarray scanner (Agilent, Palo Alto, CA, USA) and evaluated as a scatter-plot graph for gene expression.

In Situ:

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: 8 × 15K (Agilent) in situ synthesis of gene chip was used to detect gene expression. .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Synthesized:

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *
Article Snippet: After isolation, RNAs were synthesized into cDNAs using 500 ng of total RNA. cRNA was labeled with a single color (Cy3) using Quick Amp labeling kit (Agilent Technologies, Palo Alto, CA) and hybridized to an Arabidopsis oligo DNA microarray Ver. .. Arrays were scanned with a microarray scanner (G2505B, Agilent Technologies) and analyzed using GeneSpring Ver.7 (Agilent Technologies).

Software:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: .. Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent). ..

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent). .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

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
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. .. The resulting tiff images were processed using Agilent feature extraction software version 10.5.1.1 with the GE1_105_Dec08 protocol.

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Article Snippet: The signals were captured by a Microarray Scanner (G2565, Agilent Technologies, Santa Clara, USA). .. The generated data was analysed using the software Genespring 12.1 (Agilent Technologies) and Ingenuity Pathway Analysis (IPA; Qiagen).

Article Title: Redox-dependent condensation of the mycobacterial nucleoid by WhiB4
Article Snippet: .. Slides were scanned on a microarray scanner (Agilent Technologies) and analyzed using the GeneSpring software. ..

Article Title: Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen
Article Snippet: .. Data analysis The oligonucleotide probe identifiers and signal intensities from the scanned microarray image files were determined using software running on the microarray scanner (Feature Extraction, v 10.5.1.1, Agilent). ..

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: .. Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software. ..

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification. .. The data were extracted from these images using the Agilent Feature Extraction v.9.5.3 software.

Isolation:

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: Gene Chip RNA of equivalent different developmental stage flower samples from two safflower lines were isolated using trizol and purified. .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *
Article Snippet: After isolation, RNAs were synthesized into cDNAs using 500 ng of total RNA. cRNA was labeled with a single color (Cy3) using Quick Amp labeling kit (Agilent Technologies, Palo Alto, CA) and hybridized to an Arabidopsis oligo DNA microarray Ver. .. Arrays were scanned with a microarray scanner (G2505B, Agilent Technologies) and analyzed using GeneSpring Ver.7 (Agilent Technologies).

Generated:

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Article Snippet: The signals were captured by a Microarray Scanner (G2565, Agilent Technologies, Santa Clara, USA). .. The generated data was analysed using the software Genespring 12.1 (Agilent Technologies) and Ingenuity Pathway Analysis (IPA; Qiagen).

Labeling:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to custom v3.1 multi-species 8×15k miRNA arrays (Agilent). .. Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent).

Article Title: Wnt activity and basal niche position sensitize intestinal stem and progenitor cells to DNA damage
Article Snippet: 50 ng of each sample was labeled with the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. .. Slides were scanned using a microarray scanner (Agilent Technologies).

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The cyanine 3-labeled cRNA was purified with RNeasy (Qiagen) and examined for its concentration and labeling quality by a spectrophotometer. .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *
Article Snippet: After isolation, RNAs were synthesized into cDNAs using 500 ng of total RNA. cRNA was labeled with a single color (Cy3) using Quick Amp labeling kit (Agilent Technologies, Palo Alto, CA) and hybridized to an Arabidopsis oligo DNA microarray Ver. .. Arrays were scanned with a microarray scanner (G2505B, Agilent Technologies) and analyzed using GeneSpring Ver.7 (Agilent Technologies).

Article Title: Redox-dependent condensation of the mycobacterial nucleoid by WhiB4
Article Snippet: RNA amplification, cDNA labeling, microarray hybridization, scanning, and data analysis were performed at the UDSCMAC as described previously . .. Slides were scanned on a microarray scanner (Agilent Technologies) and analyzed using the GeneSpring software.

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities
Article Snippet: Labeled cRNA samples were hybridized for 17 h to 44 k Whole Human Genome DNA microarrays (G4112F, Agilent) using a hybridization oven (Agilent). .. After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent.

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: The probe-hybridization mixture contained 16.0 µl Cy3 and 16.0 µl Cy5 labeled samples and 26.2 µl hybridization mixture (60 µg yeast tRNA, 12 µg polyA and 24 µg human Cot-1 DNA). .. Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software.

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: The labeled targets were purified using the RNeasy® Mini Kit (Qiagen) and their quality and quantity were confirmed by spectrophotometry and the Bioanalyzer 2100 technology (Agilent Technologies, USA). .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

Article Title: ?9-Tetrahydrocannabinol Disrupts Estrogen-Signaling through Up-Regulation of Estrogen Receptor β (ERβ)
Article Snippet: Labeled cRNA (Cy3 to controls, Cy5 to Δ9 -THC samples) was hybridized to human oligo DNA microarray slides (Agilent, Palo Alto, CA) that are spotted with human genes. .. Specific hybridization was analyzed using a Microarray scanner (Agilent, Palo Alto, CA, USA) and evaluated as a scatter-plot graph for gene expression.

Purification:

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: Gene Chip RNA of equivalent different developmental stage flower samples from two safflower lines were isolated using trizol and purified. .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The cyanine 3-labeled cRNA was purified with RNeasy (Qiagen) and examined for its concentration and labeling quality by a spectrophotometer. .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Article Title: Redox-dependent condensation of the mycobacterial nucleoid by WhiB4
Article Snippet: At 2 h post-treatment with CHP, total RNA was purified as described . .. Slides were scanned on a microarray scanner (Agilent Technologies) and analyzed using the GeneSpring software.

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities
Article Snippet: Of the total RNA, 400 ng was transcribed into cDNA with an oligo-dT primer, followed by transcription into cRNA labeled with cyanine 3-CTP (Quick-Amp Labeling Kit, One-color, Agilent). cRNA purification was performed with the RNeasy Mini Kit (Qiagen). cRNA yields and the dye incorporation were measured with the NanoDrop-1000 spectrophotometer. .. After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent.

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: The labeled targets were purified using the RNeasy® Mini Kit (Qiagen) and their quality and quantity were confirmed by spectrophotometry and the Bioanalyzer 2100 technology (Agilent Technologies, USA). .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

Article Title: ?9-Tetrahydrocannabinol Disrupts Estrogen-Signaling through Up-Regulation of Estrogen Receptor β (ERβ)
Article Snippet: Total RNA was collected from 25 μ M Δ9 -THC or vehicle-treated MCF-7 cells 48 h after exposure by using the RNeasy kit (Qiagen, Inc. Hilden, Germany) and was purified using RNeasy/QIAamp columns (Qiagen, Inc. Hilden, Germany). .. Specific hybridization was analyzed using a Microarray scanner (Agilent, Palo Alto, CA, USA) and evaluated as a scatter-plot graph for gene expression.

Concentration Assay:

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The cyanine 3-labeled cRNA was purified with RNeasy (Qiagen) and examined for its concentration and labeling quality by a spectrophotometer. .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Incubation:

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: Cy3- and Cy5-labeled cRNA targets were mixed and incubated on microarray slides at 65°C for 17 hours. .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

Significance Assay:

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy. .. Differential genes were screened out with appropriate fold change absolutely (FCA) calculated and p-value.

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Article Snippet: The signals were captured by a Microarray Scanner (G2565, Agilent Technologies, Santa Clara, USA). .. Differentially expressed genes with statistical significance (p-value cut-off ≤ 0,005) between the two groups (clivus versus sacrum) were identified using scatter plot filtering.

Imaging:

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
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. .. The resulting tiff images were processed using Agilent feature extraction software version 10.5.1.1 with the GE1_105_Dec08 protocol.

Expressing:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: Paragraph title: Microarray and differential expression analysis ... Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent).

Article Title: Wnt activity and basal niche position sensitize intestinal stem and progenitor cells to DNA damage
Article Snippet: Quality-proved RNA with a RIN value higher than 9.0 was used for gene expression analysis, which was performed using the SurePrint G3 Mouse GE 8x60K (Design ID 028005) Microarray Kit (Agilent Technologies). .. Slides were scanned using a microarray scanner (Agilent Technologies).

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance
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). .. Feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen) resulting in a table containing individual probe signal intensities for both dyes.

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: 8 × 15K (Agilent) in situ synthesis of gene chip was used to detect gene expression. .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The microarray processing of the samples was carried out with necessary reagent kits provided by Agilent, according to the manufacturer's one-color microarray-based gene expression analysis protocol (version 5.5). .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Article Snippet: Paragraph title: Gene Expression Analysis ... The signals were captured by a Microarray Scanner (G2565, Agilent Technologies, Santa Clara, USA).

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *
Article Snippet: Arrays were scanned with a microarray scanner (G2505B, Agilent Technologies) and analyzed using GeneSpring Ver.7 (Agilent Technologies). .. These data were used for reference data of mRNA expression for corresponding proteins, which was analyzed by shotgun proteomics.

Article Title: Redox-dependent condensation of the mycobacterial nucleoid by WhiB4
Article Snippet: The total RNA was processed and hybridized to the Mtb Whole Genome Gene Expression Profiling microarray- G2509F (AMADID: G2509F_034585, Agilent Technologies PLC). .. Slides were scanned on a microarray scanner (Agilent Technologies) and analyzed using the GeneSpring software.

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software. .. The dataset is submitted to GEO gene expression omnibus (GSE50707) with platform accession number: GPL: 1397.

Article Title: ?9-Tetrahydrocannabinol Disrupts Estrogen-Signaling through Up-Regulation of Estrogen Receptor β (ERβ)
Article Snippet: .. Specific hybridization was analyzed using a Microarray scanner (Agilent, Palo Alto, CA, USA) and evaluated as a scatter-plot graph for gene expression. ..

Chromatin Immunoprecipitation:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: Microarray and differential expression analysis Probe labeling and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies ( http://www.arrays.ucsf.edu and http://www.agilent.com ). miRNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). .. Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent).

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: Paragraph title: Gene Chip ... Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Planar Chromatography:

Article Title: Redox-dependent condensation of the mycobacterial nucleoid by WhiB4
Article Snippet: The total RNA was processed and hybridized to the Mtb Whole Genome Gene Expression Profiling microarray- G2509F (AMADID: G2509F_034585, Agilent Technologies PLC). .. Slides were scanned on a microarray scanner (Agilent Technologies) and analyzed using the GeneSpring software.

Spectrophotometry:

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance
Article Snippet: The yields of amplified RNA and incorporation of CyDye were determined by using a NanoDrop spectrophotometer. .. 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).

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The cyanine 3-labeled cRNA was purified with RNeasy (Qiagen) and examined for its concentration and labeling quality by a spectrophotometer. .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities
Article Snippet: Of the total RNA, 400 ng was transcribed into cDNA with an oligo-dT primer, followed by transcription into cRNA labeled with cyanine 3-CTP (Quick-Amp Labeling Kit, One-color, Agilent). cRNA purification was performed with the RNeasy Mini Kit (Qiagen). cRNA yields and the dye incorporation were measured with the NanoDrop-1000 spectrophotometer. .. After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent.

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: The labeled targets were purified using the RNeasy® Mini Kit (Qiagen) and their quality and quantity were confirmed by spectrophotometry and the Bioanalyzer 2100 technology (Agilent Technologies, USA). .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

Microarray:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: .. Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent). ..

Article Title: Wnt activity and basal niche position sensitize intestinal stem and progenitor cells to DNA damage
Article Snippet: .. Slides were scanned using a microarray scanner (Agilent Technologies). ..

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance
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). .. Feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen) resulting in a table containing individual probe signal intensities for both dyes.

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy. .. The expression analysis of unigenes in two lines were performed by DESeq (V1.14.0) ( ).

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent). .. The microarray scan data were processed with Future Extraction software (version 9.5.1; Agilent), according to its manual.

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
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. .. The resulting tiff images were processed using Agilent feature extraction software version 10.5.1.1 with the GE1_105_Dec08 protocol.

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Article Snippet: .. The signals were captured by a Microarray Scanner (G2565, Agilent Technologies, Santa Clara, USA). .. The generated data was analysed using the software Genespring 12.1 (Agilent Technologies) and Ingenuity Pathway Analysis (IPA; Qiagen).

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *
Article Snippet: .. Arrays were scanned with a microarray scanner (G2505B, Agilent Technologies) and analyzed using GeneSpring Ver.7 (Agilent Technologies). ..

Article Title: Redox-dependent condensation of the mycobacterial nucleoid by WhiB4
Article Snippet: .. Slides were scanned on a microarray scanner (Agilent Technologies) and analyzed using the GeneSpring software. ..

Article Title: Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen
Article Snippet: .. Data analysis The oligonucleotide probe identifiers and signal intensities from the scanned microarray image files were determined using software running on the microarray scanner (Feature Extraction, v 10.5.1.1, Agilent). ..

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities
Article Snippet: .. After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent. .. Analysis of DNA microarray data The images of the scanned microarrays were processed with the Agilent Feature Extraction software.

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: .. Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software. ..

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification. .. The data were extracted from these images using the Agilent Feature Extraction v.9.5.3 software.

Article Title: ?9-Tetrahydrocannabinol Disrupts Estrogen-Signaling through Up-Regulation of Estrogen Receptor β (ERβ)
Article Snippet: .. Specific hybridization was analyzed using a Microarray scanner (Agilent, Palo Alto, CA, USA) and evaluated as a scatter-plot graph for gene expression. ..

Article Title: Genome-wide analysis of aberrantly expressed lncRNAs and miRNAs with associated co-expression and ceRNA networks in β-thalassemia and hereditary persistence of fetal hemoglobin
Article Snippet: .. The arrays were washed and immediately scanned using a microarray scanner (Axon, USA). .. Finally, the scanned images were imported into GenePix software (Axon, USA) for grid alignment and data extraction.

Derivative Assay:

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: Internal standards were derived from the Two-Color RNA Spike-in Kit (Agilent Technologies, USA). .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

Hybridization:

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance
Article Snippet: Hybridization was performed with a NimbleGen Hybridization System 4 (Roche NimbleGen) for 20 hours at 42 °C. .. 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).

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: Hybridization of the RNA was performed using the gene expression hybridization kit (Agilent). .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent). .. The microarray scan data were processed with Future Extraction software (version 9.5.1; Agilent), according to its manual.

Article Title: Redox-dependent condensation of the mycobacterial nucleoid by WhiB4
Article Snippet: RNA amplification, cDNA labeling, microarray hybridization, scanning, and data analysis were performed at the UDSCMAC as described previously . .. Slides were scanned on a microarray scanner (Agilent Technologies) and analyzed using the GeneSpring software.

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities
Article Snippet: .. After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent. .. Analysis of DNA microarray data The images of the scanned microarrays were processed with the Agilent Feature Extraction software.

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: Paragraph title: Microarray, probe generation, hybridization and washing ... Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software.

Article Title: ?9-Tetrahydrocannabinol Disrupts Estrogen-Signaling through Up-Regulation of Estrogen Receptor β (ERβ)
Article Snippet: .. Specific hybridization was analyzed using a Microarray scanner (Agilent, Palo Alto, CA, USA) and evaluated as a scatter-plot graph for gene expression. ..

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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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    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