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Agilent technologies g2565ba scanner
G2565ba Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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RNA Extraction:

Article Title: Transcription analysis on response of swine lung to H1N1 swine influenza virus
Article Snippet: Paragraph title: RNA extraction, reverse transcription, RNA labelling and cRNA hybridization Total ... Hybridization and scanning of the arrays were carried out according to standard protocols using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA).

Article Title: Investigation of Pathogenesis of H1N1 Influenza Virus and Swine Streptococcus suis Serotype 2 Co-Infection in Pigs by Microarray Analysis
Article Snippet: Agilent microarray experiment The same areas in the lungs from each group were sampled for RNA extraction using TRIzol (Invitrogen, Carlsbad, CA) and RNaeasy MiNi Kit (QIAGEN) according to the manufacturer’s instruction. .. The hybridization and scanning of the arrays were conducted using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA) according to the standard protocol.

Amplification:

Article Title: BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer
Article Snippet: Digested linker-ligated DNA was used as a template for PCR amplification (20 cycles) and coupled to fluorescent dyes. .. Detection was done on a G2565BA scanner (Agilent Technologies) and feature extraction using Feature Extraction Software version 9.5.3.1 (Agilent Technologies).

Article Title: Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer
Article Snippet: DMH was performed according to Yan et al. Cy5-labeled amplicons, representing methylated DNA fragments derived from tumours and paired normal mucosa samples, were cohybridized to the CpG island microarrays with a Cy3-labeled common reference amplicon consisting of a pool of DNA from the six colorectal cancer cell lines described above. .. Detection was done on a G2565BA scanner (Agilent Technologies, Santa Clara, CA, USA) and image analysis using GenePix6.0 (Molecular Devices, Union City, CA, USA).

Article Title: Transcription analysis on response of swine lung to H1N1 swine influenza virus
Article Snippet: Reverse transcription of 2 μg total RNA and synthesis of Cy3-labelled cRNA with one round of amplification were carried out by a commercial Agilent array service (Shanghaibio, China) following the standard one-cycle protocol according to the manufacturer's instructions. .. Hybridization and scanning of the arrays were carried out according to standard protocols using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA).

Expressing:

Article Title: Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer
Article Snippet: Detection was done on a G2565BA scanner (Agilent Technologies, Santa Clara, CA, USA) and image analysis using GenePix6.0 (Molecular Devices, Union City, CA, USA). .. Microarray data are available on Gene Expression Omnibus with accession number .

Article Title: Expression of ERCC1, TYMS, TUBB3, RRM1 and TOP2A in patients with esophageal squamous cell carcinoma: A hierarchical clustering analysis
Article Snippet: Paragraph title: MicroRNA expression profiling analysis ... The microRNA arrays were scanned using a G2565BA scanner (Agilent Technologies) and the images were analyzed using Agilent Feature Extraction software (version 10.7).

Fluorescence:

Article Title: Microarray assessment of N-glycan-specific IgE and IgG profiles associated with Schistosoma mansoni infection in rural and urban Uganda
Article Snippet: .. The slides were scanned for fluorescence at a 10μm resolution with a G2565BA scanner (Agilent Technologies, CA, USA) using 633 nm and 532 nm lasers for detection of reactivity to glycan-specific IgE and IgG, respectively. .. Data analysis Using GenePix Pro 7.0 software (Molecular Devices, CA, USA), a spot-finding algorithm was used to align and re-size fluorescence spots in the microarray images, without setting a composite pixel intensity threshold.

Article Title: Local Antiglycan Antibody Responses to Skin Stage and Migratory Schistosomula of Schistosoma japonicum
Article Snippet: Scanning was performed using a G2565BA scanner (Agilent Technologies, Santa Clara, CA) at 10-μm resolution with 2 lasers (532 nm and 633 nm). .. The median fluorescence intensities of each of the spots with background subtracted were then averaged for each glycan sample.

Methylation:

Article Title: BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer
Article Snippet: Cy5- or Cy3-labeled amplicons, representing methylated DNA fragments derived from tumor and normal samples, were co-hybridized to the Agilent 244 k human CpG island microarrays (#G4492A, Agilent Technologies) in a dye-swap setup. .. Detection was done on a G2565BA scanner (Agilent Technologies) and feature extraction using Feature Extraction Software version 9.5.3.1 (Agilent Technologies).

Article Title: Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer
Article Snippet: Paragraph title: Differential methylation hybridisation ... Detection was done on a G2565BA scanner (Agilent Technologies, Santa Clara, CA, USA) and image analysis using GenePix6.0 (Molecular Devices, Union City, CA, USA).

Software:

Article Title: Ketamine Inhalation Ameliorates Ovalbumin-Induced Murine Asthma by Suppressing the Epithelial-Mesenchymal Transition
Article Snippet: .. The samples were labeled with cyanine 3-pCp and subsequently hybridized to the Agilent mouse microRNA microarray release version 15 (1881 mouse miRNAs represented) using a microRNA Complete Labeling and Hyb Kit (Agilent Technologies) for 20 h. After washing, the slides were scanned with a G2565BA scanner, and the data were analyzed and monitored with Agilent Feature Extraction Software version 9.5.1 and GeneSpring GX software version 12.5 (Agilent Technologies). .. Real-time quantitative reverse transcription–polymerase chain reaction Total RNA was extracted from lung tissue using Trizol reagent (Invitrogen, Carlsbad, California, USA) according to the manufacturer’s instructions.

Article Title: BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer
Article Snippet: .. Detection was done on a G2565BA scanner (Agilent Technologies) and feature extraction using Feature Extraction Software version 9.5.3.1 (Agilent Technologies). ..

Article Title: Insights into Human Astrocyte Response to H5N1 Infection by Microarray Analysis
Article Snippet: .. Transcriptional profiles were assessed by 4x44K Agilent whole human genome oligo microarray (with three chips per sample).Hybridization and scanning of arrays were performed in accordance with standard protocols using a G2565BA Scanner (Agilent).Raw data were extracted with Feature Extraction software 10.7 (Agilent) and normalized using the quantile algorithm in GeneSpring GX 11.0 (Agilent). .. ANOVA, using Benjamini-Hochberg multiple testing correction, was performed to identify the genes significantly differentially expressed (DE) (p < 0.05) in response to viral infection.

Article Title: Investigation of Pathogenesis of H1N1 Influenza Virus and Swine Streptococcus suis Serotype 2 Co-Infection in Pigs by Microarray Analysis
Article Snippet: The hybridization and scanning of the arrays were conducted using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA) according to the standard protocol. .. The hybridization data were normalized using Agilent Feature Extraction Software.

Article Title: Local Antiglycan Antibody Responses to Skin Stage and Migratory Schistosomula of Schistosoma japonicum
Article Snippet: Scanning was performed using a G2565BA scanner (Agilent Technologies, Santa Clara, CA) at 10-μm resolution with 2 lasers (532 nm and 633 nm). .. The scanned images were analyzed with Genepix Pro 7.0 software.

Article Title: Multi-omic profiling of MYCN-amplified neuroblastoma cell-lines
Article Snippet: .. Briefly, 3 μg of genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the BioPrime DNA Labeling kit (Life Technologies); labeled reference and tumor DNAs were then hybridized in a SureHyb gasket (Agilent Technologies) at 65 °C for 40 h. Eventually, the slides were washed and scanned immediately after by means of a G2565BA scanner (Agilent Technologies) using the two color scan setting for 244 k slides; TIFF images were processed with the FeatureExtractor software (Agilent Technologies). .. 2.4 Transcriptome microarrays Total RNA was first extracted from cells at 80% confluence by means of the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol; it was then quantified, and its quality was assessed by using the RNA 6000 Nano assay on the 2100 Bioanalyzer (Agilent Technologies); an RNA integrity number threshold of 7 was used to select samples to be included in the study; 500 ng of starting material was eventually employed for each sample and Cyanine-3 labeled cRNA was produced.

Article Title: Multi-omic profiling of MYCN-amplified neuroblastoma cell-lines
Article Snippet: .. The RNA was Cyanine-3-labeled and samples were then hybridized on Human miRNA Microarrays 2.0 (G4470B, Agilent Technologies) in a SureHyb gasket (Agilent Technologies) at 55 °C for 20 h. Slides were then washed and immediately scanned using a G2565BA scanner (Agilent Technologies); TIFF images were eventually processed with the FeatureExtractor software (Agilent Technologies). ..

Article Title: Expression of ERCC1, TYMS, TUBB3, RRM1 and TOP2A in patients with esophageal squamous cell carcinoma: A hierarchical clustering analysis
Article Snippet: .. The microRNA arrays were scanned using a G2565BA scanner (Agilent Technologies) and the images were analyzed using Agilent Feature Extraction software (version 10.7). .. Raw data were normalized using the Quantile algorithm function of the Gene Spring Software 11.0 (Agilent Technologies).

Article Title: A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)
Article Snippet: .. Slides were scanned on a G2565BA scanner and analyzed using Agilent CGH Analytics software ver. ..

Isolation:

Article Title: Translational compensation of genomic instability in neuroblastoma
Article Snippet: aCGH microarrays Total DNA was isolated according to the manufacturer’s protocol using the DNA Blood and Tissue Extraction Kit (Qiagen). .. Array-CGH was performed using Human Genome CGH 244 K microarrays (Agilent Technologies), and the slides were scanned using a G2565BA scanner (Agilent Technologies).

Article Title: Translational compensation of genomic instability in neuroblastoma
Article Snippet: miRNA profiling miRNAs were isolated according to the manufacturer’s protocol using the miRNeasy Micro Kit (Qiagen) and then quantified and quality-assessed using the Small RNA Assay on the 2100 Bioanalyzer (Agilent Technologies); a 7 RIN threshold was used to select samples for this study. miRNA profiling was performed with 100 ng of starting material. .. The samples were hybridized on Human miRNA Microarrays 2.0 (Agilent Technologies), and the slides were scanned using a G2565BA scanner (Agilent Technologies).

Article Title: Ketamine Inhalation Ameliorates Ovalbumin-Induced Murine Asthma by Suppressing the Epithelial-Mesenchymal Transition
Article Snippet: MicroRNA array analysis Total RNA was isolated using a miRNeasy Kit (Qiagen, Valencia, California, USA) according to the manufacturer’s instructions. .. The samples were labeled with cyanine 3-pCp and subsequently hybridized to the Agilent mouse microRNA microarray release version 15 (1881 mouse miRNAs represented) using a microRNA Complete Labeling and Hyb Kit (Agilent Technologies) for 20 h. After washing, the slides were scanned with a G2565BA scanner, and the data were analyzed and monitored with Agilent Feature Extraction Software version 9.5.1 and GeneSpring GX software version 12.5 (Agilent Technologies).

Article Title: Multi-omic profiling of MYCN-amplified neuroblastoma cell-lines
Article Snippet: 2.3 aCGH microarrays Total DNA was isolated by means of the DNA Blood and Tissue Extraction Kit (Qiagen), following the manufacturer's protocol. .. Briefly, 3 μg of genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the BioPrime DNA Labeling kit (Life Technologies); labeled reference and tumor DNAs were then hybridized in a SureHyb gasket (Agilent Technologies) at 65 °C for 40 h. Eventually, the slides were washed and scanned immediately after by means of a G2565BA scanner (Agilent Technologies) using the two color scan setting for 244 k slides; TIFF images were processed with the FeatureExtractor software (Agilent Technologies).

Article Title: Multi-omic profiling of MYCN-amplified neuroblastoma cell-lines
Article Snippet: 2.6 miRome microarrays MicroRNAs from cells at 80% confluence were isolated by means of the miRNeasy Micro Kit (Qiagen), following the manufacturer's protocol. .. The RNA was Cyanine-3-labeled and samples were then hybridized on Human miRNA Microarrays 2.0 (G4470B, Agilent Technologies) in a SureHyb gasket (Agilent Technologies) at 55 °C for 20 h. Slides were then washed and immediately scanned using a G2565BA scanner (Agilent Technologies); TIFF images were eventually processed with the FeatureExtractor software (Agilent Technologies).

Article Title: Expression of ERCC1, TYMS, TUBB3, RRM1 and TOP2A in patients with esophageal squamous cell carcinoma: A hierarchical clustering analysis
Article Snippet: MicroRNA expression profiling analysis Total RNA was extracted using an RNA isolation kit (Qiagen, Inc., Valencia, CA, US), according to the manufacturer’s instructions. .. The microRNA arrays were scanned using a G2565BA scanner (Agilent Technologies) and the images were analyzed using Agilent Feature Extraction software (version 10.7).

Labeling:

Article Title: Ketamine Inhalation Ameliorates Ovalbumin-Induced Murine Asthma by Suppressing the Epithelial-Mesenchymal Transition
Article Snippet: .. The samples were labeled with cyanine 3-pCp and subsequently hybridized to the Agilent mouse microRNA microarray release version 15 (1881 mouse miRNAs represented) using a microRNA Complete Labeling and Hyb Kit (Agilent Technologies) for 20 h. After washing, the slides were scanned with a G2565BA scanner, and the data were analyzed and monitored with Agilent Feature Extraction Software version 9.5.1 and GeneSpring GX software version 12.5 (Agilent Technologies). .. Real-time quantitative reverse transcription–polymerase chain reaction Total RNA was extracted from lung tissue using Trizol reagent (Invitrogen, Carlsbad, California, USA) according to the manufacturer’s instructions.

Article Title: Insights into Human Astrocyte Response to H5N1 Infection by Microarray Analysis
Article Snippet: RNA labeling and hybridization were conducted using a commercial Agilent array service (Shanghaibio, Shanghai, China), following the standard one-cycle protocol in accordance with the manufacturer’s instructions. .. Transcriptional profiles were assessed by 4x44K Agilent whole human genome oligo microarray (with three chips per sample).Hybridization and scanning of arrays were performed in accordance with standard protocols using a G2565BA Scanner (Agilent).Raw data were extracted with Feature Extraction software 10.7 (Agilent) and normalized using the quantile algorithm in GeneSpring GX 11.0 (Agilent).

Article Title: Investigation of Pathogenesis of H1N1 Influenza Virus and Swine Streptococcus suis Serotype 2 Co-Infection in Pigs by Microarray Analysis
Article Snippet: RNA labeling and hybridization were performed using a commercial Agilent array (Shanghaibio, China) that followed the standard one-cycle protocol according to the manufacturer’s instructions. .. The hybridization and scanning of the arrays were conducted using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA) according to the standard protocol.

Article Title: Multi-omic profiling of MYCN-amplified neuroblastoma cell-lines
Article Snippet: .. Briefly, 3 μg of genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the BioPrime DNA Labeling kit (Life Technologies); labeled reference and tumor DNAs were then hybridized in a SureHyb gasket (Agilent Technologies) at 65 °C for 40 h. Eventually, the slides were washed and scanned immediately after by means of a G2565BA scanner (Agilent Technologies) using the two color scan setting for 244 k slides; TIFF images were processed with the FeatureExtractor software (Agilent Technologies). .. 2.4 Transcriptome microarrays Total RNA was first extracted from cells at 80% confluence by means of the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol; it was then quantified, and its quality was assessed by using the RNA 6000 Nano assay on the 2100 Bioanalyzer (Agilent Technologies); an RNA integrity number threshold of 7 was used to select samples to be included in the study; 500 ng of starting material was eventually employed for each sample and Cyanine-3 labeled cRNA was produced.

Real-time Polymerase Chain Reaction:

Article Title: A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)
Article Snippet: Slides were scanned on a G2565BA scanner and analyzed using Agilent CGH Analytics software ver. .. Real-time PCR was also performed to evaluate GRAMD3 gene copy number under standard conditions (exon 2, primers: 5′-ggtgtggaggagaaaaagaaagc; 5′-ggagtccgcctccacagat; TaqMan probe: 6-FAM-tgcaggtcgccaaca-Quencher).

Concentration Assay:

Article Title: Transcription analysis on response of swine lung to H1N1 swine influenza virus
Article Snippet: Both RNA integrity and concentration were evaluated by Agilent 2100 Bioanalyzer by following the manufacturer's instructions (Agilent Technologies, Palo Alto, CA). .. Hybridization and scanning of the arrays were carried out according to standard protocols using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA).

Article Title: Insights into Human Astrocyte Response to H5N1 Infection by Microarray Analysis
Article Snippet: RNA integrity and concentration were evaluated by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). .. Transcriptional profiles were assessed by 4x44K Agilent whole human genome oligo microarray (with three chips per sample).Hybridization and scanning of arrays were performed in accordance with standard protocols using a G2565BA Scanner (Agilent).Raw data were extracted with Feature Extraction software 10.7 (Agilent) and normalized using the quantile algorithm in GeneSpring GX 11.0 (Agilent).

Incubation:

Article Title: Microarray assessment of N-glycan-specific IgE and IgG profiles associated with Schistosoma mansoni infection in rural and urban Uganda
Article Snippet: After sequential washes with PBS-0.05% Tween20 and PBS, the slides were incubated for 30 minutes at RT in the dark with PromoFluor 647-labelled anti-human IgE (diluted 1/150 in PBS-0.01% Tween20) and Cy3-labelled anti-human IgG (diluted 1/1000 in PBS-0.01% Tween20), while shaking. .. The slides were scanned for fluorescence at a 10μm resolution with a G2565BA scanner (Agilent Technologies, CA, USA) using 633 nm and 532 nm lasers for detection of reactivity to glycan-specific IgE and IgG, respectively.

Article Title: Local Antiglycan Antibody Responses to Skin Stage and Migratory Schistosomula of Schistosoma japonicum
Article Snippet: The slides were subsequently rinsed with PBS-0.05% Tween 20 and PBS, followed by incubation for 30 min at room temperature with Alexa Fluor 555-labeled goat anti-rat IgG and Alexa Fluor 647-labeled goat anti-rat IgM, both diluted 1:1,000 in PBS-0.01% Tween 20 with 1% BSA. .. Scanning was performed using a G2565BA scanner (Agilent Technologies, Santa Clara, CA) at 10-μm resolution with 2 lasers (532 nm and 633 nm).

Infection:

Article Title: Transcription analysis on response of swine lung to H1N1 swine influenza virus
Article Snippet: RNA extraction, reverse transcription, RNA labelling and cRNA hybridization Total RNA extraction from the lungs prepared from the same lesion, areas of localized infection (with viral mRNA present) was performed using TRIzol by following the standard instructions (Invitrogen, Carlsbad, CA) and a clean-up was carried out using RNeasy columns (Qiagen, Valencia, CA). .. Hybridization and scanning of the arrays were carried out according to standard protocols using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA).

Article Title: Insights into Human Astrocyte Response to H5N1 Infection by Microarray Analysis
Article Snippet: Agilent Microarray Experiments U251 cells were inoculated with HM/06 at MOI1.0 or infected control. .. Transcriptional profiles were assessed by 4x44K Agilent whole human genome oligo microarray (with three chips per sample).Hybridization and scanning of arrays were performed in accordance with standard protocols using a G2565BA Scanner (Agilent).Raw data were extracted with Feature Extraction software 10.7 (Agilent) and normalized using the quantile algorithm in GeneSpring GX 11.0 (Agilent).

BAC Assay:

Article Title: A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)
Article Snippet: Slides were scanned on a G2565BA scanner and analyzed using Agilent CGH Analytics software ver. .. Array-CGH data were validated using FISH analysis on LCLs metaphase preparations from patient VI-3, using BAC probes RP11–1123C14 and RP11–1031D8 spanning the deleted region, and RP11–322L12 and RP11–638F8 overlapping the centromeric and telomeric breakpoint, respectively ( Supplementary Material, Fig. S1 ).

DNA Labeling:

Article Title: Multi-omic profiling of MYCN-amplified neuroblastoma cell-lines
Article Snippet: .. Briefly, 3 μg of genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the BioPrime DNA Labeling kit (Life Technologies); labeled reference and tumor DNAs were then hybridized in a SureHyb gasket (Agilent Technologies) at 65 °C for 40 h. Eventually, the slides were washed and scanned immediately after by means of a G2565BA scanner (Agilent Technologies) using the two color scan setting for 244 k slides; TIFF images were processed with the FeatureExtractor software (Agilent Technologies). .. 2.4 Transcriptome microarrays Total RNA was first extracted from cells at 80% confluence by means of the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol; it was then quantified, and its quality was assessed by using the RNA 6000 Nano assay on the 2100 Bioanalyzer (Agilent Technologies); an RNA integrity number threshold of 7 was used to select samples to be included in the study; 500 ng of starting material was eventually employed for each sample and Cyanine-3 labeled cRNA was produced.

Polymerase Chain Reaction:

Article Title: BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer
Article Snippet: Digested linker-ligated DNA was used as a template for PCR amplification (20 cycles) and coupled to fluorescent dyes. .. Detection was done on a G2565BA scanner (Agilent Technologies) and feature extraction using Feature Extraction Software version 9.5.3.1 (Agilent Technologies).

Fluorescence In Situ Hybridization:

Article Title: A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)
Article Snippet: Slides were scanned on a G2565BA scanner and analyzed using Agilent CGH Analytics software ver. .. Array-CGH data were validated using FISH analysis on LCLs metaphase preparations from patient VI-3, using BAC probes RP11–1123C14 and RP11–1031D8 spanning the deleted region, and RP11–322L12 and RP11–638F8 overlapping the centromeric and telomeric breakpoint, respectively ( Supplementary Material, Fig. S1 ).

Binding Assay:

Article Title: Microarray assessment of N-glycan-specific IgE and IgG profiles associated with Schistosoma mansoni infection in rural and urban Uganda
Article Snippet: The glycan antibody binding assay was adapted from existing procedures , , , , as follows: Nexterion H N-hydroxysuccinimide-coated microarray slides (Schott AG, Mainz, Germany) (pre-blocked with 50 mM ethanolamine in 50 mM sodium borate buffer pH 9.0, and stored at −20 °C) were thawed at room temperature (RT) and covered with silicone gaskets to create seven wells with printed microarrays per slide. .. The slides were scanned for fluorescence at a 10μm resolution with a G2565BA scanner (Agilent Technologies, CA, USA) using 633 nm and 532 nm lasers for detection of reactivity to glycan-specific IgE and IgG, respectively.

Microarray:

Article Title: Microarray assessment of N-glycan-specific IgE and IgG profiles associated with Schistosoma mansoni infection in rural and urban Uganda
Article Snippet: Paragraph title: Microarray detection of N-glycan-specific IgE and IgG ... The slides were scanned for fluorescence at a 10μm resolution with a G2565BA scanner (Agilent Technologies, CA, USA) using 633 nm and 532 nm lasers for detection of reactivity to glycan-specific IgE and IgG, respectively.

Article Title: Ketamine Inhalation Ameliorates Ovalbumin-Induced Murine Asthma by Suppressing the Epithelial-Mesenchymal Transition
Article Snippet: .. The samples were labeled with cyanine 3-pCp and subsequently hybridized to the Agilent mouse microRNA microarray release version 15 (1881 mouse miRNAs represented) using a microRNA Complete Labeling and Hyb Kit (Agilent Technologies) for 20 h. After washing, the slides were scanned with a G2565BA scanner, and the data were analyzed and monitored with Agilent Feature Extraction Software version 9.5.1 and GeneSpring GX software version 12.5 (Agilent Technologies). .. Real-time quantitative reverse transcription–polymerase chain reaction Total RNA was extracted from lung tissue using Trizol reagent (Invitrogen, Carlsbad, California, USA) according to the manufacturer’s instructions.

Article Title: Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer
Article Snippet: Detection was done on a G2565BA scanner (Agilent Technologies, Santa Clara, CA, USA) and image analysis using GenePix6.0 (Molecular Devices, Union City, CA, USA). .. Microarray data for the tumour and normal samples were compared using an error-weighted ANOVA model and corrected for multiple testing in Rosetta Resolver.

Article Title: Transcription analysis on response of swine lung to H1N1 swine influenza virus
Article Snippet: Transcriptional profiles were assessed using Agilent 4 × 44 K Porcine Oligo Microarray which contains more than 42,034 transcripts of pig from the database of RefSeq, Unigene and TIGR. .. Hybridization and scanning of the arrays were carried out according to standard protocols using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA).

Article Title: Insights into Human Astrocyte Response to H5N1 Infection by Microarray Analysis
Article Snippet: .. Transcriptional profiles were assessed by 4x44K Agilent whole human genome oligo microarray (with three chips per sample).Hybridization and scanning of arrays were performed in accordance with standard protocols using a G2565BA Scanner (Agilent).Raw data were extracted with Feature Extraction software 10.7 (Agilent) and normalized using the quantile algorithm in GeneSpring GX 11.0 (Agilent). .. ANOVA, using Benjamini-Hochberg multiple testing correction, was performed to identify the genes significantly differentially expressed (DE) (p < 0.05) in response to viral infection.

Article Title: Investigation of Pathogenesis of H1N1 Influenza Virus and Swine Streptococcus suis Serotype 2 Co-Infection in Pigs by Microarray Analysis
Article Snippet: Paragraph title: Agilent microarray experiment ... The hybridization and scanning of the arrays were conducted using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA) according to the standard protocol.

Article Title: Local Antiglycan Antibody Responses to Skin Stage and Migratory Schistosomula of Schistosoma japonicum
Article Snippet: Paragraph title: Glycan microarray analysis. ... Scanning was performed using a G2565BA scanner (Agilent Technologies, Santa Clara, CA) at 10-μm resolution with 2 lasers (532 nm and 633 nm).

Article Title: Multi-omic profiling of MYCN-amplified neuroblastoma cell-lines
Article Snippet: The microarray profiling was performed using 100 ng of starting material for each sample. .. The RNA was Cyanine-3-labeled and samples were then hybridized on Human miRNA Microarrays 2.0 (G4470B, Agilent Technologies) in a SureHyb gasket (Agilent Technologies) at 55 °C for 20 h. Slides were then washed and immediately scanned using a G2565BA scanner (Agilent Technologies); TIFF images were eventually processed with the FeatureExtractor software (Agilent Technologies).

Article Title: Expression of ERCC1, TYMS, TUBB3, RRM1 and TOP2A in patients with esophageal squamous cell carcinoma: A hierarchical clustering analysis
Article Snippet: All the microRNA microarray experiments were conducted using an Agilent Human miRNA microarray kit (version 16.0; Agilent Technologies). .. The microRNA arrays were scanned using a G2565BA scanner (Agilent Technologies) and the images were analyzed using Agilent Feature Extraction software (version 10.7).

Derivative Assay:

Article Title: BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer
Article Snippet: Cy5- or Cy3-labeled amplicons, representing methylated DNA fragments derived from tumor and normal samples, were co-hybridized to the Agilent 244 k human CpG island microarrays (#G4492A, Agilent Technologies) in a dye-swap setup. .. Detection was done on a G2565BA scanner (Agilent Technologies) and feature extraction using Feature Extraction Software version 9.5.3.1 (Agilent Technologies).

Article Title: Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer
Article Snippet: DMH was performed according to Yan et al. Cy5-labeled amplicons, representing methylated DNA fragments derived from tumours and paired normal mucosa samples, were cohybridized to the CpG island microarrays with a Cy3-labeled common reference amplicon consisting of a pool of DNA from the six colorectal cancer cell lines described above. .. Detection was done on a G2565BA scanner (Agilent Technologies, Santa Clara, CA, USA) and image analysis using GenePix6.0 (Molecular Devices, Union City, CA, USA).

Hybridization:

Article Title: BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer
Article Snippet: Paragraph title: Array hybridization ... Detection was done on a G2565BA scanner (Agilent Technologies) and feature extraction using Feature Extraction Software version 9.5.3.1 (Agilent Technologies).

Article Title: Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer
Article Snippet: Paragraph title: Differential methylation hybridisation ... Detection was done on a G2565BA scanner (Agilent Technologies, Santa Clara, CA, USA) and image analysis using GenePix6.0 (Molecular Devices, Union City, CA, USA).

Article Title: Transcription analysis on response of swine lung to H1N1 swine influenza virus
Article Snippet: .. Hybridization and scanning of the arrays were carried out according to standard protocols using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA). .. Expression microarray analysis and bioinformatics Raw data and statistical analyses were performed with Feature Extraction software.

Article Title: Identification of prefoldin amplification (1q23.3-q24.1) in bladder cancer using comparative genomic hybridization (CGH) arrays of urinary DNA
Article Snippet: Paragraph title: Urinary DNA labelling and hybridization to the Array-CGH platform ... Arrays were scanned at 670 and 570 nm for Cy5 and Cy3 respectively, using the G2565BA Scanner (Agilent).

Article Title: Insights into Human Astrocyte Response to H5N1 Infection by Microarray Analysis
Article Snippet: RNA labeling and hybridization were conducted using a commercial Agilent array service (Shanghaibio, Shanghai, China), following the standard one-cycle protocol in accordance with the manufacturer’s instructions. .. Transcriptional profiles were assessed by 4x44K Agilent whole human genome oligo microarray (with three chips per sample).Hybridization and scanning of arrays were performed in accordance with standard protocols using a G2565BA Scanner (Agilent).Raw data were extracted with Feature Extraction software 10.7 (Agilent) and normalized using the quantile algorithm in GeneSpring GX 11.0 (Agilent).

Article Title: Investigation of Pathogenesis of H1N1 Influenza Virus and Swine Streptococcus suis Serotype 2 Co-Infection in Pigs by Microarray Analysis
Article Snippet: .. The hybridization and scanning of the arrays were conducted using a G2565BA Scanner (Agilent Technologies, Palo Alto, CA) according to the standard protocol. .. The hybridization data were normalized using Agilent Feature Extraction Software.

Article Title: A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)
Article Snippet: Paragraph title: Array comparative genomic hybridization and breakpoint identification ... Slides were scanned on a G2565BA scanner and analyzed using Agilent CGH Analytics software ver.

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    Agilent technologies dna microarray scanner
    Effects of CNT-1 and CNT-2 on gene expression in NR8383 cells. Venn diagram showing the number of upregulated and downregulated genes in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h (A). Heat map generated from <t>DNA</t> <t>microarray</t> data reflecting differential expression of genes involved in the response to stimulus (GO: 0050896) in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h. Expression levels are colored blue for low intensity and red for high intensity (see scale at the bottom right corner) (B).
    Dna Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 1473 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Distinct effects by aging and RSV on gene expression. Panel A shows each individual animal in a principal component analysis (PCA) of the <t>microarray</t> data of lung samples derived at day 0 (mock-inoculated, black, n = 4/group), or at day 2 (red, n = 5/group) or day 5 (green, n = 5/group) after inoculation with RSV. Aging-regulated expression appears by PC1, RSV-regulated gene expression appears along PC2. Y, young (circles); O, old (triangles); M, mock control; R, RSV-inoculated. Panel B shows a Venn-diagram depicting numbers of genes that are significantly upregulated (↑), downregulated (↓), or show no significant response (−). The three symbols indicate from left to right: response to RSV in young mice, response to RSV in old mice, response to aging, respectively.
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    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.
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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