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Agilent technologies microarray scanner g2565ba
Microarray Scanner G2565ba, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 60 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 92 stars, based on 60 article reviews
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microarray scanner g2565ba - by Bioz Stars, 2020-04
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Amplification:

Article Title: STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W] [OA]
Article Snippet: Copy RNA synthesis and dye labeling were performed with a kit (Low RNA Input Linear Amplification Kit PLUS; Agilent). .. Microarray scanner G2565BA (Agilent) equipped with Feature Extraction version 9.5.1 software (Agilent) was used for scanning of the slides and extracting the data.

Article Title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars
Article Snippet: Total RNA (800 ng) was labeled with either Cy3 or Cy5 dye using an Agilent Low RNA Input Fluorescent Linear Amplification Kit. .. Hybridized microarray chips were scanned using the Agilent Microarray Scanner G2565BA.

Article Title: The RNA-Binding Protein Musashi1 Affects Medulloblastoma Growth via a Network of Cancer-Related Genes and Is an Indicator of Poor Prognosis
Article Snippet: After amplification, 750 ng of Cy3- and Cy5-labeled RNA were combined and hybridized to an Agilent Human Gene expression array (Agilent Technologies). .. Microarray slides were then scanned on an Agilent Microarray Scanner G2565BA (Agilent Technologies), and data were extracted with Agilent Feature Extraction software version 9.1 (Agilent Technologies).

Article Title: Stem cell gene expression in MRPS18-2-immortalized rat embryonic fibroblasts
Article Snippet: For each sample, 200 ng total RNA was reverse transcribed, linear amplified, and labeled with Cy3 using the one color Low RNA Input Linear Amplification Kit PLUS (Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer's instructions and purified using the RNeasy Mini kit (Agilent Technologies). .. Samples were then hybridized on Agilent 4 × 44K whole rat genome GE arrays (Agilent Design #014850) at 65°C for 17 h. After washing with GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2565BA (Agilent Technologies) at 5-μ m resolution.

Article Title: Characterization of Osteoblastic and Osteolytic Proteins in Prostate Cancer Bone Metastases
Article Snippet: Paragraph title: RNA amplification and microarray hybridization ... Fluorescence array images were collected using the Agilent microarray scanner G2565BA.

Blocking Assay:

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: Following purification, the appropriate Cy3-labeled test DNA and Cy5-labeled reference DNA were mixed together and combined with 2× Hybridization buffer (Agilent), 10× blocking agent (Agilent), and Human Cot-1 DNA (Invitrogen, Carlsbad, CA). .. After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution.

Real-time Polymerase Chain Reaction:

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution. .. Quantitative real-time PCR (qPCR) was performed to verify the abnormal aCGH findings in the proband and to test other family members, according to published guidelines [ ].

Microarray:

Article Title: STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W] [OA]
Article Snippet: .. Microarray scanner G2565BA (Agilent) equipped with Feature Extraction version 9.5.1 software (Agilent) was used for scanning of the slides and extracting the data. .. Data mining and statistical analyses for microarray data were performed using GeneSpring GX version 7.3.1 (Agilent).

Article Title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars
Article Snippet: .. Hybridized microarray chips were scanned using the Agilent Microarray Scanner G2565BA. .. To detect differentially expressed significant genes between control and treated samples, each slide image was processed by Agilent Feature Extraction software (version 9.5.3.1).

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: .. After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution. .. Captured images were transformed to data with Feature Extraction Software, version 9.5 (Agilent), and then imported into Agilent CGH Analytics 3.2.5 software for analysis.

Article Title: The RNA-Binding Protein Musashi1 Affects Medulloblastoma Growth via a Network of Cancer-Related Genes and Is an Indicator of Poor Prognosis
Article Snippet: .. Microarray slides were then scanned on an Agilent Microarray Scanner G2565BA (Agilent Technologies), and data were extracted with Agilent Feature Extraction software version 9.1 (Agilent Technologies). .. All analyses were performed within the R/Bioconductor software (R Foundation for Statistical Computing, Vienna, Austria).

Article Title: Rs12976445 Polymorphism Is Associated with Post-Ablation Recurrence of Atrial Fibrillation by Modulating the Expression of MicroRNA-125a and Interleukin-6R
Article Snippet: .. An Agilent Microarray scanner G2565BA (Agilent Technologies, Santa Clara, CA) was utilized to detect hybridization signals, which were then quantified using Agilent Feature extraction software version 9.5.1 (Agilent Technologies). .. A commercially available QuantStudio 12K Flex instrument (Thermo Fisher Scientific; formerly Life Technologies, Grand Island, NY) was used to perform TaqMan assays and identify the rs12976445 genotype of all samples.

Article Title: Stem cell gene expression in MRPS18-2-immortalized rat embryonic fibroblasts
Article Snippet: .. Samples were then hybridized on Agilent 4 × 44K whole rat genome GE arrays (Agilent Design #014850) at 65°C for 17 h. After washing with GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2565BA (Agilent Technologies) at 5-μ m resolution. .. Feature extraction software (Version 9.5.3.1) was used to convert the image into gene expression data.

Article Title: A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)
Article Snippet: .. Scanning was performed using an Agilent Microarray Scanner G2565BA. .. Outlier spots and spot intensity for Cy3 and Cy5 channels were extracted using Agilent Feature Extraction software version 10.7.

Article Title: Early Trypanosoma cruzi Infection Triggers mTORC1-Mediated Respiration Increase and Mitochondrial Biogenesis in Human Primary Cardiomyocytes
Article Snippet: .. The slides were scanned using an Agilent microarray scanner G2565BA at default settings for all parameters. .. We used Agilent Feature Extraction (version 9.5.1) for quality control, data filtering, and data normalization.

Article Title: Characterization of Osteoblastic and Osteolytic Proteins in Prostate Cancer Bone Metastases
Article Snippet: .. Fluorescence array images were collected using the Agilent microarray scanner G2565BA. .. Agilent Feature Extraction software was used to grid, extract, and normalize data.

Article Title: Two-color Dye-swap DNA Microarray approach toward confident gene expression profiling in PMCAO mouse model for ischemia-related and PACAP38-influenced genes
Article Snippet: .. Hybridization and wash processes were performed according to the manufacturer's instructions, and hybridized microarrays were scanned using an Agilent Microarray scanner G2565BA or G2505C (Agilent Technologies). .. For the detection of significant differentially expressed genes between control and treated samples each slide image was processed by Agilent Feature Extraction software (version 9.5.3.1 or 11.0.1.1, Agilent Technologies).

Article Title: Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes
Article Snippet: .. After two washing steps, the arrays were dried and scanned using the Agilent Microarray Scanner G2565BA (Agilent Technologies, Santa Clara, CA, USA) with 3 µm resolution in double-pass mode. .. Resulting tif-files were analyzed with the Agilent AGW Feature Extraction software (version 10.10.11, Agilent Technologies).

Two Tailed Test:

Article Title: Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes
Article Snippet: After two washing steps, the arrays were dried and scanned using the Agilent Microarray Scanner G2565BA (Agilent Technologies, Santa Clara, CA, USA) with 3 µm resolution in double-pass mode. .. We identified differentially expressed miRNAs in blastemal WTs, regressive WTs and all WT samples combined, each compared to the four normal kidney samples via an unpaired two-tailed t -test.

Significance Assay:

Article Title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars
Article Snippet: Hybridized microarray chips were scanned using the Agilent Microarray Scanner G2565BA. .. The significance (P) value is based on the propagate error and universal error models.

Expressing:

Article Title: The RNA-Binding Protein Musashi1 Affects Medulloblastoma Growth via a Network of Cancer-Related Genes and Is an Indicator of Poor Prognosis
Article Snippet: After amplification, 750 ng of Cy3- and Cy5-labeled RNA were combined and hybridized to an Agilent Human Gene expression array (Agilent Technologies). .. Microarray slides were then scanned on an Agilent Microarray Scanner G2565BA (Agilent Technologies), and data were extracted with Agilent Feature Extraction software version 9.1 (Agilent Technologies).

Article Title: Rs12976445 Polymorphism Is Associated with Post-Ablation Recurrence of Atrial Fibrillation by Modulating the Expression of MicroRNA-125a and Interleukin-6R
Article Snippet: A Human microRNA microarray V2 (Agilent Technologies, Santa Clara, California, USA) containing 76 human viral microRNAs and 723 human microRNAs (Sanger database V.10.1) was utilized to measure the microRNA expression profiles in the samples. .. An Agilent Microarray scanner G2565BA (Agilent Technologies, Santa Clara, CA) was utilized to detect hybridization signals, which were then quantified using Agilent Feature extraction software version 9.5.1 (Agilent Technologies).

Article Title: Stem cell gene expression in MRPS18-2-immortalized rat embryonic fibroblasts
Article Snippet: Samples were then hybridized on Agilent 4 × 44K whole rat genome GE arrays (Agilent Design #014850) at 65°C for 17 h. After washing with GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2565BA (Agilent Technologies) at 5-μ m resolution. .. Feature extraction software (Version 9.5.3.1) was used to convert the image into gene expression data.

Article Title: A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)
Article Snippet: After assessing successful dye incorporation and sample integrity, 2.5 μg of each labelled sample was hybridised to the custom-made oligo-microarray at 65 °C for 17 h following Gene Expression Hybridization Kit instructions. .. Scanning was performed using an Agilent Microarray Scanner G2565BA.

Article Title: Early Trypanosoma cruzi Infection Triggers mTORC1-Mediated Respiration Increase and Mitochondrial Biogenesis in Human Primary Cardiomyocytes
Article Snippet: Microarray analysis was performed by using a Human Gene Expression 8x60K v2 Microarray (Agilent) in a one-color design. .. The slides were scanned using an Agilent microarray scanner G2565BA at default settings for all parameters.

Article Title: Characterization of Osteoblastic and Osteolytic Proteins in Prostate Cancer Bone Metastases
Article Snippet: A total of 825 ng of amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) and hybridized to custom Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols. .. Fluorescence array images were collected using the Agilent microarray scanner G2565BA.

Article Title: Two-color Dye-swap DNA Microarray approach toward confident gene expression profiling in PMCAO mouse model for ischemia-related and PACAP38-influenced genes
Article Snippet: As also elegantly explained by Dombkowski and co-workers in 2004, dye orientation has a significant influence on the measurements and inferences of differential gene expression most probably due to the labeling method, and further suggesting that until dye bias effects can be explained the dye-swap approach is important in microarray reference designs . .. Hybridization and wash processes were performed according to the manufacturer's instructions, and hybridized microarrays were scanned using an Agilent Microarray scanner G2565BA or G2505C (Agilent Technologies).

Article Title: Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes
Article Snippet: Paragraph title: 4.3. miRNA Expression Profile ... After two washing steps, the arrays were dried and scanned using the Agilent Microarray Scanner G2565BA (Agilent Technologies, Santa Clara, CA, USA) with 3 µm resolution in double-pass mode.

Genome Wide:

Article Title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars
Article Snippet: A rice 4 × 44K custom (eARRAY, AMAdid-017845) oligo DNA microarray chip (G2514F: Agilent Technologies, Palo Alto, CA, USA) was used for genome-wide gene profiling as described previously. .. Hybridized microarray chips were scanned using the Agilent Microarray Scanner G2565BA.

Transformation Assay:

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution. .. Captured images were transformed to data with Feature Extraction Software, version 9.5 (Agilent), and then imported into Agilent CGH Analytics 3.2.5 software for analysis.

Hybridization:

Article Title: STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W] [OA]
Article Snippet: Competitive hybridization analyses (Cy3-labeled versus Cy5-labeled copy RNA samples) were performed between control (24 h, no Al at pH 5.0) and rhizotoxin-treated (24 h in pH 4.5 solution or 10 μ m Al solution at pH 5.0) samples of Col-4, and comparisons were made between Col-0 and the stop1 mutant in both treatments. .. Microarray scanner G2565BA (Agilent) equipped with Feature Extraction version 9.5.1 software (Agilent) was used for scanning of the slides and extracting the data.

Article Title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars
Article Snippet: Hybridization and wash processes were performed according to the manufacturer’s instructions. .. Hybridized microarray chips were scanned using the Agilent Microarray Scanner G2565BA.

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: The hybridization mixture was slowly dispensed to a microarray chip and assembled with an Agilent SureHyb chamber. .. After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution.

Article Title: Rs12976445 Polymorphism Is Associated with Post-Ablation Recurrence of Atrial Fibrillation by Modulating the Expression of MicroRNA-125a and Interleukin-6R
Article Snippet: .. An Agilent Microarray scanner G2565BA (Agilent Technologies, Santa Clara, CA) was utilized to detect hybridization signals, which were then quantified using Agilent Feature extraction software version 9.5.1 (Agilent Technologies). .. A commercially available QuantStudio 12K Flex instrument (Thermo Fisher Scientific; formerly Life Technologies, Grand Island, NY) was used to perform TaqMan assays and identify the rs12976445 genotype of all samples.

Article Title: A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)
Article Snippet: Paragraph title: Microarray design, hybridization and data analysis ... Scanning was performed using an Agilent Microarray Scanner G2565BA.

Article Title: Characterization of Osteoblastic and Osteolytic Proteins in Prostate Cancer Bone Metastases
Article Snippet: Paragraph title: RNA amplification and microarray hybridization ... Fluorescence array images were collected using the Agilent microarray scanner G2565BA.

Article Title: Two-color Dye-swap DNA Microarray approach toward confident gene expression profiling in PMCAO mouse model for ischemia-related and PACAP38-influenced genes
Article Snippet: .. Hybridization and wash processes were performed according to the manufacturer's instructions, and hybridized microarrays were scanned using an Agilent Microarray scanner G2565BA or G2505C (Agilent Technologies). .. For the detection of significant differentially expressed genes between control and treated samples each slide image was processed by Agilent Feature Extraction software (version 9.5.3.1 or 11.0.1.1, Agilent Technologies).

Indirect Immunoperoxidase Assay:

Article Title: Stem cell gene expression in MRPS18-2-immortalized rat embryonic fibroblasts
Article Snippet: Samples were then hybridized on Agilent 4 × 44K whole rat genome GE arrays (Agilent Design #014850) at 65°C for 17 h. After washing with GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2565BA (Agilent Technologies) at 5-μ m resolution. .. Molecular functions of genes were classified according to Gene Ontology function using Ingenuity Pathway Analysis (IPA).

Polymerase Chain Reaction:

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: The superimposed mutant PCR products were subcloned into pGEM-T vector (Promega, Madison, WI) and sequenced to identify the mutation. .. After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution.

Fluorescence:

Article Title: Characterization of Osteoblastic and Osteolytic Proteins in Prostate Cancer Bone Metastases
Article Snippet: .. Fluorescence array images were collected using the Agilent microarray scanner G2565BA. .. Agilent Feature Extraction software was used to grid, extract, and normalize data.

Mutagenesis:

Article Title: STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W] [OA]
Article Snippet: Competitive hybridization analyses (Cy3-labeled versus Cy5-labeled copy RNA samples) were performed between control (24 h, no Al at pH 5.0) and rhizotoxin-treated (24 h in pH 4.5 solution or 10 μ m Al solution at pH 5.0) samples of Col-4, and comparisons were made between Col-0 and the stop1 mutant in both treatments. .. Microarray scanner G2565BA (Agilent) equipped with Feature Extraction version 9.5.1 software (Agilent) was used for scanning of the slides and extracting the data.

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: The superimposed mutant PCR products were subcloned into pGEM-T vector (Promega, Madison, WI) and sequenced to identify the mutation. .. After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution.

Isolation:

Article Title: Early Trypanosoma cruzi Infection Triggers mTORC1-Mediated Respiration Increase and Mitochondrial Biogenesis in Human Primary Cardiomyocytes
Article Snippet: The labeled cRNA was purified with Illustra RNAspin Mini Isolation kit (GE Healthcare, United States). .. The slides were scanned using an Agilent microarray scanner G2565BA at default settings for all parameters.

Article Title: Characterization of Osteoblastic and Osteolytic Proteins in Prostate Cancer Bone Metastases
Article Snippet: Two micrograms reference total RNA was amplified two rounds while 500 ng total RNA isolated from either osteoblastic or osteolytic bone metastatic cores was amplified one round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), incorporating amino-allyl UTP into amplified antisense RNA. .. Fluorescence array images were collected using the Agilent microarray scanner G2565BA.

Labeling:

Article Title: STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W] [OA]
Article Snippet: Copy RNA synthesis and dye labeling were performed with a kit (Low RNA Input Linear Amplification Kit PLUS; Agilent). .. Microarray scanner G2565BA (Agilent) equipped with Feature Extraction version 9.5.1 software (Agilent) was used for scanning of the slides and extracting the data.

Article Title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars
Article Snippet: Total RNA (800 ng) was labeled with either Cy3 or Cy5 dye using an Agilent Low RNA Input Fluorescent Linear Amplification Kit. .. Hybridized microarray chips were scanned using the Agilent Microarray Scanner G2565BA.

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: The digested test DNA and reference DNA were labeled with cyanine (Cy)3-deoxyuridine triphosphate (dUTP) or Cy5-dUTP, respectively. .. After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution.

Article Title: The RNA-Binding Protein Musashi1 Affects Medulloblastoma Growth via a Network of Cancer-Related Genes and Is an Indicator of Poor Prognosis
Article Snippet: Two hundred nanograms of RNA from each sample was labeled with Cy3 or Cy5 dye using an Agilent Low RNA Input Linear Amplification Kit (Agilent Technologies) according to manufacturer protocol. .. Microarray slides were then scanned on an Agilent Microarray Scanner G2565BA (Agilent Technologies), and data were extracted with Agilent Feature Extraction software version 9.1 (Agilent Technologies).

Article Title: Rs12976445 Polymorphism Is Associated with Post-Ablation Recurrence of Atrial Fibrillation by Modulating the Expression of MicroRNA-125a and Interleukin-6R
Article Snippet: A Mirna Labeling Reagent and a hybridization kit (Agilent Technologies, Santa Clara, California, USA) were utilized to pre-treat the samples. .. An Agilent Microarray scanner G2565BA (Agilent Technologies, Santa Clara, CA) was utilized to detect hybridization signals, which were then quantified using Agilent Feature extraction software version 9.5.1 (Agilent Technologies).

Article Title: Stem cell gene expression in MRPS18-2-immortalized rat embryonic fibroblasts
Article Snippet: After labeling, samples were measured on a Nanodrop microarray module for labeling efficiency and quantification. .. Samples were then hybridized on Agilent 4 × 44K whole rat genome GE arrays (Agilent Design #014850) at 65°C for 17 h. After washing with GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2565BA (Agilent Technologies) at 5-μ m resolution.

Article Title: A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)
Article Snippet: Briefly, for each sample 200 ng of total RNA was labelled with Cy3 or Cy5 using Low Input Quick Amp Labeling Kit . .. Scanning was performed using an Agilent Microarray Scanner G2565BA.

Article Title: Early Trypanosoma cruzi Infection Triggers mTORC1-Mediated Respiration Increase and Mitochondrial Biogenesis in Human Primary Cardiomyocytes
Article Snippet: The labeled cRNA was purified with Illustra RNAspin Mini Isolation kit (GE Healthcare, United States). .. The slides were scanned using an Agilent microarray scanner G2565BA at default settings for all parameters.

Article Title: Characterization of Osteoblastic and Osteolytic Proteins in Prostate Cancer Bone Metastases
Article Snippet: A total of 825 ng of amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) and hybridized to custom Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols. .. Fluorescence array images were collected using the Agilent microarray scanner G2565BA.

Article Title: Two-color Dye-swap DNA Microarray approach toward confident gene expression profiling in PMCAO mouse model for ischemia-related and PACAP38-influenced genes
Article Snippet: As also elegantly explained by Dombkowski and co-workers in 2004, dye orientation has a significant influence on the measurements and inferences of differential gene expression most probably due to the labeling method, and further suggesting that until dye bias effects can be explained the dye-swap approach is important in microarray reference designs . .. Hybridization and wash processes were performed according to the manufacturer's instructions, and hybridized microarrays were scanned using an Agilent Microarray scanner G2565BA or G2505C (Agilent Technologies).

Article Title: Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes
Article Snippet: The labeled RNA for each sample was hybridized to the microarray for 20 h at 55 °C with 20 rpm rotation in the SureHyb chambers (Agilent). .. After two washing steps, the arrays were dried and scanned using the Agilent Microarray Scanner G2565BA (Agilent Technologies, Santa Clara, CA, USA) with 3 µm resolution in double-pass mode.

Purification:

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: Following purification, the appropriate Cy3-labeled test DNA and Cy5-labeled reference DNA were mixed together and combined with 2× Hybridization buffer (Agilent), 10× blocking agent (Agilent), and Human Cot-1 DNA (Invitrogen, Carlsbad, CA). .. After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution.

Article Title: Stem cell gene expression in MRPS18-2-immortalized rat embryonic fibroblasts
Article Snippet: For each sample, 200 ng total RNA was reverse transcribed, linear amplified, and labeled with Cy3 using the one color Low RNA Input Linear Amplification Kit PLUS (Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer's instructions and purified using the RNeasy Mini kit (Agilent Technologies). .. Samples were then hybridized on Agilent 4 × 44K whole rat genome GE arrays (Agilent Design #014850) at 65°C for 17 h. After washing with GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2565BA (Agilent Technologies) at 5-μ m resolution.

Article Title: A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)
Article Snippet: Labelled cRNA was purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany) and quantified using a NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA). .. Scanning was performed using an Agilent Microarray Scanner G2565BA.

Article Title: Early Trypanosoma cruzi Infection Triggers mTORC1-Mediated Respiration Increase and Mitochondrial Biogenesis in Human Primary Cardiomyocytes
Article Snippet: The labeled cRNA was purified with Illustra RNAspin Mini Isolation kit (GE Healthcare, United States). .. The slides were scanned using an Agilent microarray scanner G2565BA at default settings for all parameters.

Chromatin Immunoprecipitation:

Article Title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars
Article Snippet: A rice 4 × 44K custom (eARRAY, AMAdid-017845) oligo DNA microarray chip (G2514F: Agilent Technologies, Palo Alto, CA, USA) was used for genome-wide gene profiling as described previously. .. Hybridized microarray chips were scanned using the Agilent Microarray Scanner G2565BA.

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: The hybridization mixture was slowly dispensed to a microarray chip and assembled with an Agilent SureHyb chamber. .. After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution.

Plasmid Preparation:

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: The superimposed mutant PCR products were subcloned into pGEM-T vector (Promega, Madison, WI) and sequenced to identify the mutation. .. After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution.

Software:

Article Title: STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W]STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities 1 [C] [W] [OA]
Article Snippet: .. Microarray scanner G2565BA (Agilent) equipped with Feature Extraction version 9.5.1 software (Agilent) was used for scanning of the slides and extracting the data. .. Data mining and statistical analyses for microarray data were performed using GeneSpring GX version 7.3.1 (Agilent).

Article Title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars
Article Snippet: Hybridized microarray chips were scanned using the Agilent Microarray Scanner G2565BA. .. To detect differentially expressed significant genes between control and treated samples, each slide image was processed by Agilent Feature Extraction software (version 9.5.3.1).

Article Title: A 556 kb deletion in the downstream region of the PAX6 gene causes familial aniridia and other eye anomalies in a Chinese family
Article Snippet: After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution. .. Captured images were transformed to data with Feature Extraction Software, version 9.5 (Agilent), and then imported into Agilent CGH Analytics 3.2.5 software for analysis.

Article Title: The RNA-Binding Protein Musashi1 Affects Medulloblastoma Growth via a Network of Cancer-Related Genes and Is an Indicator of Poor Prognosis
Article Snippet: .. Microarray slides were then scanned on an Agilent Microarray Scanner G2565BA (Agilent Technologies), and data were extracted with Agilent Feature Extraction software version 9.1 (Agilent Technologies). .. All analyses were performed within the R/Bioconductor software (R Foundation for Statistical Computing, Vienna, Austria).

Article Title: Rs12976445 Polymorphism Is Associated with Post-Ablation Recurrence of Atrial Fibrillation by Modulating the Expression of MicroRNA-125a and Interleukin-6R
Article Snippet: .. An Agilent Microarray scanner G2565BA (Agilent Technologies, Santa Clara, CA) was utilized to detect hybridization signals, which were then quantified using Agilent Feature extraction software version 9.5.1 (Agilent Technologies). .. A commercially available QuantStudio 12K Flex instrument (Thermo Fisher Scientific; formerly Life Technologies, Grand Island, NY) was used to perform TaqMan assays and identify the rs12976445 genotype of all samples.

Article Title: Stem cell gene expression in MRPS18-2-immortalized rat embryonic fibroblasts
Article Snippet: Samples were then hybridized on Agilent 4 × 44K whole rat genome GE arrays (Agilent Design #014850) at 65°C for 17 h. After washing with GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2565BA (Agilent Technologies) at 5-μ m resolution. .. Feature extraction software (Version 9.5.3.1) was used to convert the image into gene expression data.

Article Title: A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)
Article Snippet: Scanning was performed using an Agilent Microarray Scanner G2565BA. .. Outlier spots and spot intensity for Cy3 and Cy5 channels were extracted using Agilent Feature Extraction software version 10.7.

Article Title: Early Trypanosoma cruzi Infection Triggers mTORC1-Mediated Respiration Increase and Mitochondrial Biogenesis in Human Primary Cardiomyocytes
Article Snippet: The slides were scanned using an Agilent microarray scanner G2565BA at default settings for all parameters. .. Data processing was performed using GeneSpring GX software package (version 12.0, Agilent Technologies).

Article Title: Two-color Dye-swap DNA Microarray approach toward confident gene expression profiling in PMCAO mouse model for ischemia-related and PACAP38-influenced genes
Article Snippet: Hybridization and wash processes were performed according to the manufacturer's instructions, and hybridized microarrays were scanned using an Agilent Microarray scanner G2565BA or G2505C (Agilent Technologies). .. For the detection of significant differentially expressed genes between control and treated samples each slide image was processed by Agilent Feature Extraction software (version 9.5.3.1 or 11.0.1.1, Agilent Technologies).

Article Title: Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes
Article Snippet: After two washing steps, the arrays were dried and scanned using the Agilent Microarray Scanner G2565BA (Agilent Technologies, Santa Clara, CA, USA) with 3 µm resolution in double-pass mode. .. Resulting tif-files were analyzed with the Agilent AGW Feature Extraction software (version 10.10.11, Agilent Technologies).

RNA Extraction:

Article Title: Early Trypanosoma cruzi Infection Triggers mTORC1-Mediated Respiration Increase and Mitochondrial Biogenesis in Human Primary Cardiomyocytes
Article Snippet: Paragraph title: RNA Extraction and Gene Profiling ... The slides were scanned using an Agilent microarray scanner G2565BA at default settings for all parameters.

Selection:

Article Title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars
Article Snippet: - The dye-swap approach, which is well established in our laboratories and research, , , , - provides a more stringent selection condition for profiling differentially expressed genes rather than simply doing only 2 or 3 replicates, which overlook the dye bias. .. Hybridized microarray chips were scanned using the Agilent Microarray Scanner G2565BA.

Spectrophotometry:

Article Title: A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)
Article Snippet: Labelled cRNA was purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany) and quantified using a NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA). .. Scanning was performed using an Agilent Microarray Scanner G2565BA.

Article Title: Early Trypanosoma cruzi Infection Triggers mTORC1-Mediated Respiration Increase and Mitochondrial Biogenesis in Human Primary Cardiomyocytes
Article Snippet: The quality of each cRNA sample was verified by total yield and specificity calculated based on NanoDrop ND-1000 spectrophotometer measurements (NanoDrop Technologies, United States). .. The slides were scanned using an Agilent microarray scanner G2565BA at default settings for all parameters.

Fluorescence In Situ Hybridization:

Article Title: A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)
Article Snippet: A double loop hybridisation with dye swap experimental design was adopted with n = 4 fish per condition (starvation and feeding with diets HLL, MHL and LLH) and a total of 16 hybridisations (8 per tissue) [ ]. .. Scanning was performed using an Agilent Microarray Scanner G2565BA.

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  • 99
    Agilent technologies dna microarray scanner
    Effects of CNT-1 and CNT-2 on gene expression in NR8383 cells. Venn diagram showing the number of upregulated and downregulated genes in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h (A). Heat map generated from <t>DNA</t> <t>microarray</t> data reflecting differential expression of genes involved in the response to stimulus (GO: 0050896) in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h. Expression levels are colored blue for low intensity and red for high intensity (see scale at the bottom right corner) (B).
    Dna Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 1473 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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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    93
    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: 93/100, 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