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Agilent technologies fluorescent signal intensities
Fluorescent Signal Intensities, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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fluorescent signal intensities - by Bioz Stars, 2020-04
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Related Articles

Clone Assay:

Article Title: Transcriptomic Characterization, Chemosensitivity and Regulatory Effects of Exosomes in Spontaneous EMT/MET Transitions of Breast Cancer Cells
Article Snippet: To produce Cy3- labeled complementary RNA (cRNA), 550 ng of total RNA from the three cell clones, were labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) following the manufacturer’s protocol. .. The Cy3-labeled samples were hybridized to Agilent Whole human genome 4X44K microarrays at 65˚C for 18 h. Fluorescent signal intensities were detected using the Agilent Scan Control 7.0 Software on an Agilent DNA Microarray Scanner, at a resolution of 2 μm.

Synthesized:

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: RNA integrity was examined with the Experion Automated Electrophoresis Station (Bio-Rad). cDNA synthesis, hybridization, washing and scanning were performed by IMGM Laboratories ( www.imgm.com ) as follows: 500 ng of total RNA were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies), which serve as internal labelling control for linearity, sensitivity and accuracy. .. Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Blocking Assay:

Article Title: Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus
Article Snippet: Human Cot-1 DNA was added to block the repetitive sequences in the genomic DNA. .. Fluorescent signal intensities for both dyes were detected on an Agilent DNA Microarray Scanner using Scan Control A8.4.1 Software (Agilent Technologies).

Electrophoresis:

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: RNA integrity was examined with the Experion Automated Electrophoresis Station (Bio-Rad). cDNA synthesis, hybridization, washing and scanning were performed by IMGM Laboratories ( www.imgm.com ) as follows: 500 ng of total RNA were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies), which serve as internal labelling control for linearity, sensitivity and accuracy. .. Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Microarray:

Article Title: Exposure of Bifidobacterium longum subsp. infantis to Milk Oligosaccharides Increases Adhesion to Epithelial Cells and Induces a Substantial Transcriptional Response
Article Snippet: .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) and the design file 033172_D_F_20110831.xml. .. Analysis of Microarray Data The raw microarray results were analysed using the Limma package of the R statistics suite.

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: .. Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies). .. Normalization and analysis of microarray data were carried out using the Limma package .

Article Title: Effects of Extreme Dilutions of Apis mellifica Preparations on Gene Expression Profiles of Human Cells
Article Snippet: .. After washing, fluorescent signal intensities were detected using the Agilent Scan Control 7.0 Software on an Agilent DNA Microarray Scanner, at a resolution of 2 μm. .. Data were acquired using Agilent Feature Extraction 9.5.3.1 software.

Article Title: Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus
Article Snippet: .. Fluorescent signal intensities for both dyes were detected on an Agilent DNA Microarray Scanner using Scan Control A8.4.1 Software (Agilent Technologies). .. Images were extracted using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Article Title: Transcriptome analysis of the mouse E14.5 (TS23) developing humerus and differential expression in muscle-less mutant embryos lacking mechanical stimulation
Article Snippet: .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies). .. A workflow of the individual protocol followed for microarray preparation can be seen in .

Article Title: Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways
Article Snippet: .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies). .. The software tools Feature Extraction 10.7.3.1, GeneSpring GX 11.5.1 and Spotfire Decision Site 9.1.2 (TIBCO) were used for quality control and statistical data analysis.

Article Title: New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression
Article Snippet: .. Fluorescent signal intensities were detected with Agilent's Microarray Scanner System (Agilent Technologies) and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). .. For determination of differential miRNA expression FES derived output data files were further analyzed using the GeneSpringGX software (Agilent Technologies).

Article Title: Transcriptomic Characterization, Chemosensitivity and Regulatory Effects of Exosomes in Spontaneous EMT/MET Transitions of Breast Cancer Cells
Article Snippet: .. The Cy3-labeled samples were hybridized to Agilent Whole human genome 4X44K microarrays at 65˚C for 18 h. Fluorescent signal intensities were detected using the Agilent Scan Control 7.0 Software on an Agilent DNA Microarray Scanner, at a resolution of 2 μm. .. Microarray analysis was performed on 3 independent biological replicates for each cell clone.

Article Title: MicroRNA expression profiling for the prediction of resistance to neoadjuvant radiochemotherapy in squamous cell carcinoma of the esophagus
Article Snippet: .. Fluorescent signal intensities were detected using Scan Control A.8.4.1 Software (Agilent Technologies) in the Agilent DNA Microarray Scanner. .. For validation of the microarray data, differentially expressed miRNAs were investigated by qRT-PCR using the miRCURY LNA™ Universal RT microRNA PCR system (Exiqon A/S, Denmark).

Article Title: The presence of extra chromosomes leads to genomic instability
Article Snippet: .. Fluorescent signal intensities for both dyes were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies). .. The software Feature Extraction 10.5.1.1 as well as the software Genomic Workbench 5.0.14 was used for quality control, statistical data analysis and visualization.

Article Title: Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression
Article Snippet: .. Fluorescent signal intensities were detected on an Agilent Microarray Scanner (Agilent Technologies) with the Scan Control A.8.4.1 Software (Agilent Technologies) and were extracted from the images using the Feature Extraction 10.7.3.1 Software (Agilent Technologies). .. Microarray data analysis The raw gene expression and miRNAs microarray data were normalized using the GeneSpring GX software version 12.0 (Agilent Technologies).

Article Title: microRNAs expression profile related with response to preoperative radiochemotherapy in patients with locally advanced gastric cancer
Article Snippet: .. Fluorescent signal intensities were measured on an Agilent DNA Microarray Scanner (Cat # G2565BA; Agilent Technologies) using the Scan Control A.8.4.1 Software (Agilent Technologies), and images were extracted using the Feature Extraction 10.7.3.1 Software (Agilent Technologies). ..

Activity Assay:

Article Title: Exposure of Bifidobacterium longum subsp. infantis to Milk Oligosaccharides Increases Adhesion to Epithelial Cells and Induces a Substantial Transcriptional Response
Article Snippet: Only samples with cRNA yields > 825 ng and with a specific activity of 9.0 pmol cyanine3 per microgram of cRNA were used for array analysis. .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) and the design file 033172_D_F_20110831.xml.

Article Title: Transcriptome analysis of the mouse E14.5 (TS23) developing humerus and differential expression in muscle-less mutant embryos lacking mechanical stimulation
Article Snippet: All cRNA was quality control checked to asses yield and activity prior to hybridisation. .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

Expressing:

Article Title: Exposure of Bifidobacterium longum subsp. infantis to Milk Oligosaccharides Increases Adhesion to Epithelial Cells and Induces a Substantial Transcriptional Response
Article Snippet: Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile. .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) and the design file 033172_D_F_20110831.xml.

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: Following cRNAclean-up and quantification (NanoDrop ND-1000), 1.65 µg of each Cyanine-3-labeled cRNA sample was fragmented and prepared for One-Color based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). cRNA samples were hybridized at 65°C for 17 h on separate Tomato Gene Expression Microarrays 4×44K (Agilent Technology) containing 43803 probes, corresponding to about 33000 tomato genes (expressed sequences). .. Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Article Title: Effects of Extreme Dilutions of Apis mellifica Preparations on Gene Expression Profiles of Human Cells
Article Snippet: Paragraph title: Gene Expression Analysis ... After washing, fluorescent signal intensities were detected using the Agilent Scan Control 7.0 Software on an Agilent DNA Microarray Scanner, at a resolution of 2 μm.

Article Title: Transcriptome analysis of the mouse E14.5 (TS23) developing humerus and differential expression in muscle-less mutant embryos lacking mechanical stimulation
Article Snippet: Microarrays were then washed with increased stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with Acetonitrile (Sigma). .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

Article Title: Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways
Article Snippet: Microarrays were then washed with increased stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with Acetonitrile (Sigma). .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

Article Title: New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression
Article Snippet: Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies, Santa Clara, USA). .. Fluorescent signal intensities were detected with Agilent's Microarray Scanner System (Agilent Technologies) and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA).

Article Title: MicroRNA expression profiling for the prediction of resistance to neoadjuvant radiochemotherapy in squamous cell carcinoma of the esophagus
Article Snippet: Thereafter, the microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA). .. Fluorescent signal intensities were detected using Scan Control A.8.4.1 Software (Agilent Technologies) in the Agilent DNA Microarray Scanner.

Article Title: Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression
Article Snippet: After washing the microarray slides with buffers with increasing stringency (Gene Expression Wash Buffers; Agilent Technologies), the slides were dried with acetonitrile. .. Fluorescent signal intensities were detected on an Agilent Microarray Scanner (Agilent Technologies) with the Scan Control A.8.4.1 Software (Agilent Technologies) and were extracted from the images using the Feature Extraction 10.7.3.1 Software (Agilent Technologies).

Genome Wide:

Article Title: Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways
Article Snippet: Genome wide expression profiling was carried out using the Agilent Mouse GE v2 Microarrays (4x44K format) (G4846A, Agilent Technologies) which contains 39,485 coding and non-coding sequences of the mouse genome (Figure B). .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

Derivative Assay:

Article Title: New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression
Article Snippet: Fluorescent signal intensities were detected with Agilent's Microarray Scanner System (Agilent Technologies) and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). .. For determination of differential miRNA expression FES derived output data files were further analyzed using the GeneSpringGX software (Agilent Technologies).

Hybridization:

Article Title: Exposure of Bifidobacterium longum subsp. infantis to Milk Oligosaccharides Increases Adhesion to Epithelial Cells and Induces a Substantial Transcriptional Response
Article Snippet: Following cRNA clean-up and quantification (NanoDrop), 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for One-Color based hybridization (Gene Expression Hybridization Kit, Agilent Technologies, Co. Cork, Ireland). cRNA samples were hybridized at 65°C for 17 hrs on separate custom Bifidobacterium GE Microarrays (8×15K format). .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) and the design file 033172_D_F_20110831.xml.

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: Following cRNAclean-up and quantification (NanoDrop ND-1000), 1.65 µg of each Cyanine-3-labeled cRNA sample was fragmented and prepared for One-Color based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). cRNA samples were hybridized at 65°C for 17 h on separate Tomato Gene Expression Microarrays 4×44K (Agilent Technology) containing 43803 probes, corresponding to about 33000 tomato genes (expressed sequences). .. Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Article Title: Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus
Article Snippet: Paragraph title: Microarray hybridization ... Fluorescent signal intensities for both dyes were detected on an Agilent DNA Microarray Scanner using Scan Control A8.4.1 Software (Agilent Technologies).

Article Title: Transcriptome analysis of the mouse E14.5 (TS23) developing humerus and differential expression in muscle-less mutant embryos lacking mechanical stimulation
Article Snippet: The cRNA was cleaned up and quantified and 1.65 μg of each Cyanine-3-labelled cRNA sample was fragmented and prepared for one-colour based hybridisation (Gene Expression Hybridisation Kit, Agilent Technologies). .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

Article Title: Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways
Article Snippet: A one-colour based hybridisation protocol was performed at 65°C for 17 hours on separate mouse GE v2 microarray platforms. .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

Article Title: New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression
Article Snippet: Paragraph title: Hybridization of human miRNA microarrays ... Fluorescent signal intensities were detected with Agilent's Microarray Scanner System (Agilent Technologies) and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA).

Article Title: MicroRNA expression profiling for the prediction of resistance to neoadjuvant radiochemotherapy in squamous cell carcinoma of the esophagus
Article Snippet: Paragraph title: Preparation of cyanine-3 labeled miRNA and microarray hybridization ... Fluorescent signal intensities were detected using Scan Control A.8.4.1 Software (Agilent Technologies) in the Agilent DNA Microarray Scanner.

Article Title: The presence of extra chromosomes leads to genomic instability
Article Snippet: Paragraph title: Array comparative genomic hybridization ... Fluorescent signal intensities for both dyes were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Article Title: Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression
Article Snippet: The cyanine 3-labeled miRNA samples were subsequently prepared for one-color hybridization (miRNA Complete Labeling and Hyb Kit). .. Fluorescent signal intensities were detected on an Agilent Microarray Scanner (Agilent Technologies) with the Scan Control A.8.4.1 Software (Agilent Technologies) and were extracted from the images using the Feature Extraction 10.7.3.1 Software (Agilent Technologies).

Fluorescence:

Article Title: Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus
Article Snippet: Before scanning, each slide was washed in a drying and stabilization solution (Agilent Technologies) to stabilize the fluorescence for future scans. .. Fluorescent signal intensities for both dyes were detected on an Agilent DNA Microarray Scanner using Scan Control A8.4.1 Software (Agilent Technologies).

Mutagenesis:

Article Title: Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways
Article Snippet: Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies). .. Welch’s approximate t-test (“unpaired unequal variance”, parametric) was applied to compare the control and mutant groups.

Labeling:

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: The spiked total RNA was reverse transcribed into cDNA and then converted into labelled cRNA by in vitro transcription (Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP. cRNA concentration (ng/µl), RNA absorbance ratio (260 nm/280 nm) and Cyanine-3 dye concentration (pmol/µl) were checked for all cRNA samples using the NanoDrop ND-1000 UV-VIS spectrophotometer. .. Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Article Title: Effects of Extreme Dilutions of Apis mellifica Preparations on Gene Expression Profiles of Human Cells
Article Snippet: To produce Cy3-labeled complementary RNA (cRNA), the RNA samples were labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. .. After washing, fluorescent signal intensities were detected using the Agilent Scan Control 7.0 Software on an Agilent DNA Microarray Scanner, at a resolution of 2 μm.

Article Title: New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression
Article Snippet: Labeled miRNA samples were hybridized overnight (20 h, 55°C) to Agilent Human microRNA Microarrays 8x60K v19 using Agilent's recommended hybridization chamber and oven. .. Fluorescent signal intensities were detected with Agilent's Microarray Scanner System (Agilent Technologies) and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA).

Article Title: Transcriptomic Characterization, Chemosensitivity and Regulatory Effects of Exosomes in Spontaneous EMT/MET Transitions of Breast Cancer Cells
Article Snippet: To produce Cy3- labeled complementary RNA (cRNA), 550 ng of total RNA from the three cell clones, were labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) following the manufacturer’s protocol. .. The Cy3-labeled samples were hybridized to Agilent Whole human genome 4X44K microarrays at 65˚C for 18 h. Fluorescent signal intensities were detected using the Agilent Scan Control 7.0 Software on an Agilent DNA Microarray Scanner, at a resolution of 2 μm.

Article Title: MicroRNA expression profiling for the prediction of resistance to neoadjuvant radiochemotherapy in squamous cell carcinoma of the esophagus
Article Snippet: Paragraph title: Preparation of cyanine-3 labeled miRNA and microarray hybridization ... Fluorescent signal intensities were detected using Scan Control A.8.4.1 Software (Agilent Technologies) in the Agilent DNA Microarray Scanner.

Article Title: The presence of extra chromosomes leads to genomic instability
Article Snippet: The digested gDNA samples were directly labelled with exo-Klenow fragments and random primers by incorporation of Cy-5 dUTP (dUTP=2′-deoxyuridine 5′-triphosphate) for the experimental samples and Cy-3 dUTP for the reference samples (Genomic DNA Enzymatic Labeling Kit, Agilent Technologies). .. Fluorescent signal intensities for both dyes were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Article Title: Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression
Article Snippet: The labeled miRNA samples were hybridized to the Agilent Human miRNA Microarray 8×60K Release 16.0 (Release 16.0, 8×60K format; Agilent Technologies) for 20 h at 55°C. .. Fluorescent signal intensities were detected on an Agilent Microarray Scanner (Agilent Technologies) with the Scan Control A.8.4.1 Software (Agilent Technologies) and were extracted from the images using the Feature Extraction 10.7.3.1 Software (Agilent Technologies).

Chromatin Immunoprecipitation:

Article Title: microRNAs expression profile related with response to preoperative radiochemotherapy in patients with locally advanced gastric cancer
Article Snippet: Paragraph title: Chip scan and data acquisition ... Fluorescent signal intensities were measured on an Agilent DNA Microarray Scanner (Cat # G2565BA; Agilent Technologies) using the Scan Control A.8.4.1 Software (Agilent Technologies), and images were extracted using the Feature Extraction 10.7.3.1 Software (Agilent Technologies).

Software:

Article Title: Exposure of Bifidobacterium longum subsp. infantis to Milk Oligosaccharides Increases Adhesion to Epithelial Cells and Induces a Substantial Transcriptional Response
Article Snippet: .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) and the design file 033172_D_F_20110831.xml. .. Analysis of Microarray Data The raw microarray results were analysed using the Limma package of the R statistics suite.

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: .. Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies). .. Normalization and analysis of microarray data were carried out using the Limma package .

Article Title: Effects of Extreme Dilutions of Apis mellifica Preparations on Gene Expression Profiles of Human Cells
Article Snippet: .. After washing, fluorescent signal intensities were detected using the Agilent Scan Control 7.0 Software on an Agilent DNA Microarray Scanner, at a resolution of 2 μm. .. Data were acquired using Agilent Feature Extraction 9.5.3.1 software.

Article Title: Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus
Article Snippet: .. Fluorescent signal intensities for both dyes were detected on an Agilent DNA Microarray Scanner using Scan Control A8.4.1 Software (Agilent Technologies). .. Images were extracted using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Article Title: Transcriptome analysis of the mouse E14.5 (TS23) developing humerus and differential expression in muscle-less mutant embryos lacking mechanical stimulation
Article Snippet: .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies). .. A workflow of the individual protocol followed for microarray preparation can be seen in .

Article Title: Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways
Article Snippet: .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies). .. The software tools Feature Extraction 10.7.3.1, GeneSpring GX 11.5.1 and Spotfire Decision Site 9.1.2 (TIBCO) were used for quality control and statistical data analysis.

Article Title: New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression
Article Snippet: .. Fluorescent signal intensities were detected with Agilent's Microarray Scanner System (Agilent Technologies) and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). .. For determination of differential miRNA expression FES derived output data files were further analyzed using the GeneSpringGX software (Agilent Technologies).

Article Title: Transcriptomic Characterization, Chemosensitivity and Regulatory Effects of Exosomes in Spontaneous EMT/MET Transitions of Breast Cancer Cells
Article Snippet: .. The Cy3-labeled samples were hybridized to Agilent Whole human genome 4X44K microarrays at 65˚C for 18 h. Fluorescent signal intensities were detected using the Agilent Scan Control 7.0 Software on an Agilent DNA Microarray Scanner, at a resolution of 2 μm. .. Microarray analysis was performed on 3 independent biological replicates for each cell clone.

Article Title: MicroRNA expression profiling for the prediction of resistance to neoadjuvant radiochemotherapy in squamous cell carcinoma of the esophagus
Article Snippet: .. Fluorescent signal intensities were detected using Scan Control A.8.4.1 Software (Agilent Technologies) in the Agilent DNA Microarray Scanner. .. For validation of the microarray data, differentially expressed miRNAs were investigated by qRT-PCR using the miRCURY LNA™ Universal RT microRNA PCR system (Exiqon A/S, Denmark).

Article Title: The presence of extra chromosomes leads to genomic instability
Article Snippet: .. Fluorescent signal intensities for both dyes were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies). .. The software Feature Extraction 10.5.1.1 as well as the software Genomic Workbench 5.0.14 was used for quality control, statistical data analysis and visualization.

Article Title: Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression
Article Snippet: .. Fluorescent signal intensities were detected on an Agilent Microarray Scanner (Agilent Technologies) with the Scan Control A.8.4.1 Software (Agilent Technologies) and were extracted from the images using the Feature Extraction 10.7.3.1 Software (Agilent Technologies). .. Microarray data analysis The raw gene expression and miRNAs microarray data were normalized using the GeneSpring GX software version 12.0 (Agilent Technologies).

Article Title: microRNAs expression profile related with response to preoperative radiochemotherapy in patients with locally advanced gastric cancer
Article Snippet: .. Fluorescent signal intensities were measured on an Agilent DNA Microarray Scanner (Cat # G2565BA; Agilent Technologies) using the Scan Control A.8.4.1 Software (Agilent Technologies), and images were extracted using the Feature Extraction 10.7.3.1 Software (Agilent Technologies). ..

RNA Extraction:

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: Paragraph title: RNA extraction and microarray experiment ... Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Agarose Gel Electrophoresis:

Article Title: The presence of extra chromosomes leads to genomic instability
Article Snippet: An amount of 1 μg of gDNA was used for each reaction. gDNA integrity was tested on an 1.0% agarose gel stained with ethidium bromide. .. Fluorescent signal intensities for both dyes were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

In Vitro:

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: The spiked total RNA was reverse transcribed into cDNA and then converted into labelled cRNA by in vitro transcription (Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP. cRNA concentration (ng/µl), RNA absorbance ratio (260 nm/280 nm) and Cyanine-3 dye concentration (pmol/µl) were checked for all cRNA samples using the NanoDrop ND-1000 UV-VIS spectrophotometer. .. Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Article Title: Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways
Article Snippet: 100 ng of total RNA per sample was reverse transcribed into cDNA and then converted into labelled cRNA by in vitro transcription incorporating cyanine-3-CTP (Low input quick-amp labelling kit one-colour, Agilent Technologies). .. Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

Spectrophotometry:

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: The spiked total RNA was reverse transcribed into cDNA and then converted into labelled cRNA by in vitro transcription (Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP. cRNA concentration (ng/µl), RNA absorbance ratio (260 nm/280 nm) and Cyanine-3 dye concentration (pmol/µl) were checked for all cRNA samples using the NanoDrop ND-1000 UV-VIS spectrophotometer. .. Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Article Title: Effects of Extreme Dilutions of Apis mellifica Preparations on Gene Expression Profiles of Human Cells
Article Snippet: Yields of cRNA and the dye incorporation rate were measured with NanoPhotometer spectrophotometer (IMPLEN). .. After washing, fluorescent signal intensities were detected using the Agilent Scan Control 7.0 Software on an Agilent DNA Microarray Scanner, at a resolution of 2 μm.

Article Title: The presence of extra chromosomes leads to genomic instability
Article Snippet: Genomic DNA extracted from HCT116 was used as a reference for the high-density CGH analysis of HCT116 5/4 by the 2 × 400K array. gDNA concentration and DNA absorbance ratio (260 nm/280 nm) were measured by NanoDrop ND-1000 ultraviolet–visible spectrophotometer (PeqLab). .. Fluorescent signal intensities for both dyes were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Concentration Assay:

Article Title: Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection
Article Snippet: The spiked total RNA was reverse transcribed into cDNA and then converted into labelled cRNA by in vitro transcription (Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP. cRNA concentration (ng/µl), RNA absorbance ratio (260 nm/280 nm) and Cyanine-3 dye concentration (pmol/µl) were checked for all cRNA samples using the NanoDrop ND-1000 UV-VIS spectrophotometer. .. Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Article Title: The presence of extra chromosomes leads to genomic instability
Article Snippet: Genomic DNA extracted from HCT116 was used as a reference for the high-density CGH analysis of HCT116 5/4 by the 2 × 400K array. gDNA concentration and DNA absorbance ratio (260 nm/280 nm) were measured by NanoDrop ND-1000 ultraviolet–visible spectrophotometer (PeqLab). .. Fluorescent signal intensities for both dyes were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

Staining:

Article Title: The presence of extra chromosomes leads to genomic instability
Article Snippet: An amount of 1 μg of gDNA was used for each reaction. gDNA integrity was tested on an 1.0% agarose gel stained with ethidium bromide. .. Fluorescent signal intensities for both dyes were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

T-Test:

Article Title: Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways
Article Snippet: Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) in the Agilent DNA microarray scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies). .. Welch’s approximate t-test (“unpaired unequal variance”, parametric) was applied to compare the control and mutant groups.

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