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Agilent technologies dna microarray scanner g2565ca
Dna Microarray Scanner G2565ca, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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dna microarray scanner g2565ca - by Bioz Stars, 2020-04
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Centrifugation:

Article Title: Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806
Article Snippet: Cell pellets obtained after centrifugation (10 min, 4,600 × g ) were used for the isolation of total RNA with the phenol-based single-step method according to Chomczynski et al. , using either QIAzol (Qiagen) (microarray experiments) or TRIzol reagent (Life Technologies) (RT-qPCR) according to the manufacturers' protocols. .. MicroElute cleanup kit) and testing for Cy-dye incorporation efficiency (NanoDrop ND-1000; measurements were compared to those for control samples), Cy3- and Cy5-labeled cDNAs were hybridized to custom Microcystis sp. strain PCC 7806 microarrays (for array specifications, see “Microarray design” below) for 20 h at 65°C using a NimbleGen hybridization system 4 (NimbleGen/Roche) and scanned afterwards with an Agilent Technologies DNA microarray scanner G2565CA. cDNA preparation for RT-qPCR followed a different protocol.

Amplification:

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: 600ng of Cy 3-labeled, amplified cRNA with a specific activity of above 6 were used for subsequent hybridization following the steps of the One-color Microarray-Based Gene Expression Analysis protocol (Agilent). .. Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent).

Article Title: A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis
Article Snippet: Total RNA (0.2 μg) was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies). .. The fluorescence signals were detected by an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 10.7.1.1 software.

Article Title: Changes in Bowel Microbiota Induced by Feeding Weanlings Resistant Starch Stimulate Transcriptomic and Physiological Responses
Article Snippet: Cy3-labeled cRNA probes, synthesized from sample RNA, and Cy5-labeled probes, synthesized from reference RNA, were prepared with Low RNA Input Linear Amplification kits (Agilent Technologies) and hybridized to 4x44K Agilent Whole Rat Genome Oligo Microarrays (Agilent Technologies; G4131F) using previously described methods ( ). .. The microarrays were scanned with an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 9.0 Image Analysis software (Agilent Technologies).

Expressing:

Article Title: Gene Expression Profiling in a Mouse Model Identifies Fetal Liver- and Placenta-Derived Potential Biomarkers for Down Syndrome Screening
Article Snippet: .. Afterwards, the slides were washed according to the Nimblegen Arrays User's Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). .. Feature extraction was performed with NimbleScan v2.5 (Roche Nimblegen).

Article Title: Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression
Article Snippet: The dual color hybridization of the microarray chips was performed according to Agilent protocol GE2_105_Jan09 for two-color microarray-based gene expression analysis except that hybridization and washing was performed at 37°C. .. The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies.

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: 600ng of Cy 3-labeled, amplified cRNA with a specific activity of above 6 were used for subsequent hybridization following the steps of the One-color Microarray-Based Gene Expression Analysis protocol (Agilent). .. Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent).

Article Title: A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis
Article Snippet: Agilent Arabidopsis (V4) Gene Expression Microarray 4×44k chips were used in this study. .. The fluorescence signals were detected by an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 10.7.1.1 software.

Article Title: Germline TP53 mutations result into a constitutive defect of p53 DNA binding and transcriptional response to DNA damage
Article Snippet: Paragraph title: Comparative gene expression profiling ... Following co-hybridization, microarrays were scanned (DNA microarray scanner G2565CA, Agilent Technologies) with a resolution of 5 µm.

Article Title: A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure
Article Snippet: .. Afterwards, the slides were washed according to the Roche NimbleGen Arrays User's Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a DNA microarray scanner G2565CA (Agilent Technologies). .. Feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen).

Article Title: Transcriptional repression of DNA repair genes is a hallmark and a cause of cellular senescence
Article Snippet: Transcriptome analysis of HMEC-MEK, treated or not with 100 nM 4-OHT to induce MEK expression, were performed using Whole Human Genome Oligo 4 × 44 K Microarrays (Agilent Technologies) and the one-color gene expression Agilent workflow. .. Microarrays were washed and scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).

Article Title: Gene Expression Changes in the Olfactory Bulb of Mice Induced by Exposure to Diesel Exhaust Are Dependent on Animal Rearing Environment
Article Snippet: .. After hybridization with fluorescent-labeled cDNA, the microarray was washed using Gene Expression Wash Buffers Pack (Agilent Technologies) and then scanned by a DNA microarray Scanner G2565CA (Agilent Technologies). .. Scanner output images were normalized and digitalized by Agilent Feature Extraction software according to the Minimum Information about a Microarray Experiment guidelines and a pre-processing method for Agilent data .

Synthesized:

Article Title: Germline TP53 mutations result into a constitutive defect of p53 DNA binding and transcriptional response to DNA damage
Article Snippet: Briefly, starting from 100 ng of total RNA,cRNA was synthesized and labelled using the low input Quick Amp Labeling Kit (Agilent), with Cy3 (for untreated cells) and Cy5 (for treated cells). .. Following co-hybridization, microarrays were scanned (DNA microarray scanner G2565CA, Agilent Technologies) with a resolution of 5 µm.

Article Title: Transcriptional repression of DNA repair genes is a hallmark and a cause of cellular senescence
Article Snippet: Briefly, cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies). .. Microarrays were washed and scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).

Article Title: Changes in Bowel Microbiota Induced by Feeding Weanlings Resistant Starch Stimulate Transcriptomic and Physiological Responses
Article Snippet: Cy3-labeled cRNA probes, synthesized from sample RNA, and Cy5-labeled probes, synthesized from reference RNA, were prepared with Low RNA Input Linear Amplification kits (Agilent Technologies) and hybridized to 4x44K Agilent Whole Rat Genome Oligo Microarrays (Agilent Technologies; G4131F) using previously described methods ( ). .. The microarrays were scanned with an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 9.0 Image Analysis software (Agilent Technologies).

Quantitative RT-PCR:

Article Title: Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806
Article Snippet: .. MicroElute cleanup kit) and testing for Cy-dye incorporation efficiency (NanoDrop ND-1000; measurements were compared to those for control samples), Cy3- and Cy5-labeled cDNAs were hybridized to custom Microcystis sp. strain PCC 7806 microarrays (for array specifications, see “Microarray design” below) for 20 h at 65°C using a NimbleGen hybridization system 4 (NimbleGen/Roche) and scanned afterwards with an Agilent Technologies DNA microarray scanner G2565CA. cDNA preparation for RT-qPCR followed a different protocol. .. After DNA digestion and test PCRs, total RNA quality was checked by RNA agarose gel electrophoresis.

Microarray:

Article Title: Outer Membrane Vesicles of a Human Commensal Mediate Immune Regulation and Disease Protection
Article Snippet: .. Microarrays were analyzed using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1. ..

Article Title: Gene Expression Profiling in a Mouse Model Identifies Fetal Liver- and Placenta-Derived Potential Biomarkers for Down Syndrome Screening
Article Snippet: .. Afterwards, the slides were washed according to the Nimblegen Arrays User's Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). .. Feature extraction was performed with NimbleScan v2.5 (Roche Nimblegen).

Article Title: Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression
Article Snippet: .. The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. ..

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: .. Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent). .. The resultant microarray TIF images were processed to run batch extractions by choosing the appropriate grid using Agilent’s Feature Extraction Software version 11.0.

Article Title: A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis
Article Snippet: .. The fluorescence signals were detected by an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 10.7.1.1 software. .. Three biological repeats were conducted using cDNAs obtained from Ler and proatcape1 in 1/2 MS medium and with 12h of 125mM NaCl treatment.

Article Title: Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806
Article Snippet: .. MicroElute cleanup kit) and testing for Cy-dye incorporation efficiency (NanoDrop ND-1000; measurements were compared to those for control samples), Cy3- and Cy5-labeled cDNAs were hybridized to custom Microcystis sp. strain PCC 7806 microarrays (for array specifications, see “Microarray design” below) for 20 h at 65°C using a NimbleGen hybridization system 4 (NimbleGen/Roche) and scanned afterwards with an Agilent Technologies DNA microarray scanner G2565CA. cDNA preparation for RT-qPCR followed a different protocol. .. After DNA digestion and test PCRs, total RNA quality was checked by RNA agarose gel electrophoresis.

Article Title: Germline TP53 mutations result into a constitutive defect of p53 DNA binding and transcriptional response to DNA damage
Article Snippet: .. Following co-hybridization, microarrays were scanned (DNA microarray scanner G2565CA, Agilent Technologies) with a resolution of 5 µm. .. For each experiment, comparative gene expression profiling was performed in 2 replicates.

Article Title: A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure
Article Snippet: .. Afterwards, the slides were washed according to the Roche NimbleGen Arrays User's Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a DNA microarray scanner G2565CA (Agilent Technologies). .. Feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen).

Article Title: Transcriptional repression of DNA repair genes is a hallmark and a cause of cellular senescence
Article Snippet: .. Microarrays were washed and scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies). .. Fluorescent signals were extracted and normalized using the Feature Extraction Software Version 10.5.1.1 (Agilent Technologies), then transferred to the Genespring GX 12.6 software (Agilent Technologies) for data processing and data mining.

Article Title: Gene Expression Changes in the Olfactory Bulb of Mice Induced by Exposure to Diesel Exhaust Are Dependent on Animal Rearing Environment
Article Snippet: .. After hybridization with fluorescent-labeled cDNA, the microarray was washed using Gene Expression Wash Buffers Pack (Agilent Technologies) and then scanned by a DNA microarray Scanner G2565CA (Agilent Technologies). .. Scanner output images were normalized and digitalized by Agilent Feature Extraction software according to the Minimum Information about a Microarray Experiment guidelines and a pre-processing method for Agilent data .

Article Title: Changes in Bowel Microbiota Induced by Feeding Weanlings Resistant Starch Stimulate Transcriptomic and Physiological Responses
Article Snippet: .. The microarrays were scanned with an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 9.0 Image Analysis software (Agilent Technologies). ..

Article Title: MicroRNA-214 promotes hepatic stellate cell activation and liver fibrosis by suppressing Sufu expression
Article Snippet: .. Hybridization signals were detected by DNA microarray scanner G2565CA (Agilent Technologies, Santa Clara, CA, USA), and the scanned images were analyzed using Agilent Feature Extraction software (version 10.7). .. Liver histopathology and fibrosis measurement Excised rat or mouse liver tissues were fixed in 4% paraformaldehyde, embedded in paraffin, and sectioned, followed by staining with H & E (Beyotime, Shanghai, China), trichrome (Masson) stain kit (Baso Diagnostics Inc., Zhuhai, China), or ORO staining (Beyotime, Shanghai, China).

Activity Assay:

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: 600ng of Cy 3-labeled, amplified cRNA with a specific activity of above 6 were used for subsequent hybridization following the steps of the One-color Microarray-Based Gene Expression Analysis protocol (Agilent). .. Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent).

Mass Spectrometry:

Article Title: A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis
Article Snippet: The fluorescence signals were detected by an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 10.7.1.1 software. .. Three biological repeats were conducted using cDNAs obtained from Ler and proatcape1 in 1/2 MS medium and with 12h of 125mM NaCl treatment.

Hybridization:

Article Title: Outer Membrane Vesicles of a Human Commensal Mediate Immune Regulation and Disease Protection
Article Snippet: Paragraph title: Microarray Hybridization and Data Analysis ... Microarrays were analyzed using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1.

Article Title: Gene Expression Profiling in a Mouse Model Identifies Fetal Liver- and Placenta-Derived Potential Biomarkers for Down Syndrome Screening
Article Snippet: Paragraph title: Microarray hybridization, scanning & data processing ... Afterwards, the slides were washed according to the Nimblegen Arrays User's Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies).

Article Title: Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression
Article Snippet: The dual color hybridization of the microarray chips was performed according to Agilent protocol GE2_105_Jan09 for two-color microarray-based gene expression analysis except that hybridization and washing was performed at 37°C. .. The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies.

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: Paragraph title: Microarray material, hybridization and data analysis ... Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent).

Article Title: A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis
Article Snippet: Labelling of cDNA probes and hybridization experiments were performed according to the single-colour microarray protocols provided by the manufacturer. .. The fluorescence signals were detected by an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 10.7.1.1 software.

Article Title: Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806
Article Snippet: .. MicroElute cleanup kit) and testing for Cy-dye incorporation efficiency (NanoDrop ND-1000; measurements were compared to those for control samples), Cy3- and Cy5-labeled cDNAs were hybridized to custom Microcystis sp. strain PCC 7806 microarrays (for array specifications, see “Microarray design” below) for 20 h at 65°C using a NimbleGen hybridization system 4 (NimbleGen/Roche) and scanned afterwards with an Agilent Technologies DNA microarray scanner G2565CA. cDNA preparation for RT-qPCR followed a different protocol. .. After DNA digestion and test PCRs, total RNA quality was checked by RNA agarose gel electrophoresis.

Article Title: A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure
Article Snippet: Hybridization samples were loaded onto the microarrays and hybridized for 18 hours at 42°C with the Roche NimbleGen Hybridization System 4. .. Afterwards, the slides were washed according to the Roche NimbleGen Arrays User's Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a DNA microarray scanner G2565CA (Agilent Technologies).

Article Title: Gene Expression Changes in the Olfactory Bulb of Mice Induced by Exposure to Diesel Exhaust Are Dependent on Animal Rearing Environment
Article Snippet: .. After hybridization with fluorescent-labeled cDNA, the microarray was washed using Gene Expression Wash Buffers Pack (Agilent Technologies) and then scanned by a DNA microarray Scanner G2565CA (Agilent Technologies). .. Scanner output images were normalized and digitalized by Agilent Feature Extraction software according to the Minimum Information about a Microarray Experiment guidelines and a pre-processing method for Agilent data .

Article Title: Changes in Bowel Microbiota Induced by Feeding Weanlings Resistant Starch Stimulate Transcriptomic and Physiological Responses
Article Snippet: Only samples with an RNA integrity number of > 8.0 were used for microarray hybridization. .. The microarrays were scanned with an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 9.0 Image Analysis software (Agilent Technologies).

Article Title: MicroRNA-214 promotes hepatic stellate cell activation and liver fibrosis by suppressing Sufu expression
Article Snippet: .. Hybridization signals were detected by DNA microarray scanner G2565CA (Agilent Technologies, Santa Clara, CA, USA), and the scanned images were analyzed using Agilent Feature Extraction software (version 10.7). .. Liver histopathology and fibrosis measurement Excised rat or mouse liver tissues were fixed in 4% paraformaldehyde, embedded in paraffin, and sectioned, followed by staining with H & E (Beyotime, Shanghai, China), trichrome (Masson) stain kit (Baso Diagnostics Inc., Zhuhai, China), or ORO staining (Beyotime, Shanghai, China).

Sequencing:

Article Title: Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression
Article Snippet: The probes consisted of 2 × 22 nucleotide sequences antisense to mature miRNAs separated by a spacer of 8 nucleotides (CGATCTTT) and with a second spacer with the same sequence at the end. .. The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies.

Cell Culture:

Article Title: MicroRNA-214 promotes hepatic stellate cell activation and liver fibrosis by suppressing Sufu expression
Article Snippet: Microarray analysis Total RNAs were isolated from quiescent (cultured for 1 day) and activated (cultured for 12 days) primary HSCs, respectively, using TRIzol reagent (Life Technologies, Grand Island, NY, USA) and purified using mirVana™ miRNA Isolation Kit (Life Technologies, Grand Island, NY, USA). .. Hybridization signals were detected by DNA microarray scanner G2565CA (Agilent Technologies, Santa Clara, CA, USA), and the scanned images were analyzed using Agilent Feature Extraction software (version 10.7).

Random Primed:

Article Title: Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806
Article Snippet: Following an RNA integrity check with an RNA 6000 Nano chip on a 2100 Bioanalyzer (Agilent Technologies), 3 to 5 μg of DNA-free total RNA samples for microarrays served as templates in random primed reverse transcription reactions (Superscript II RT; Life Technologies) incorporating Cy3- and Cy5-labeled dUTPs into cDNA products of control and treatment samples, respectively. .. MicroElute cleanup kit) and testing for Cy-dye incorporation efficiency (NanoDrop ND-1000; measurements were compared to those for control samples), Cy3- and Cy5-labeled cDNAs were hybridized to custom Microcystis sp. strain PCC 7806 microarrays (for array specifications, see “Microarray design” below) for 20 h at 65°C using a NimbleGen hybridization system 4 (NimbleGen/Roche) and scanned afterwards with an Agilent Technologies DNA microarray scanner G2565CA. cDNA preparation for RT-qPCR followed a different protocol.

Polymerase Chain Reaction:

Article Title: Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806
Article Snippet: DNase-treated RNA samples yielding no PCR products ( mcyA -specific primers; for details, see Table S2 in the supplemental material) were considered DNA free and were used in downstream reactions. .. MicroElute cleanup kit) and testing for Cy-dye incorporation efficiency (NanoDrop ND-1000; measurements were compared to those for control samples), Cy3- and Cy5-labeled cDNAs were hybridized to custom Microcystis sp. strain PCC 7806 microarrays (for array specifications, see “Microarray design” below) for 20 h at 65°C using a NimbleGen hybridization system 4 (NimbleGen/Roche) and scanned afterwards with an Agilent Technologies DNA microarray scanner G2565CA. cDNA preparation for RT-qPCR followed a different protocol.

Fluorescence:

Article Title: A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis
Article Snippet: .. The fluorescence signals were detected by an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 10.7.1.1 software. .. Three biological repeats were conducted using cDNAs obtained from Ler and proatcape1 in 1/2 MS medium and with 12h of 125mM NaCl treatment.

Isolation:

Article Title: Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806
Article Snippet: Paragraph title: RNA isolation and processing. ... MicroElute cleanup kit) and testing for Cy-dye incorporation efficiency (NanoDrop ND-1000; measurements were compared to those for control samples), Cy3- and Cy5-labeled cDNAs were hybridized to custom Microcystis sp. strain PCC 7806 microarrays (for array specifications, see “Microarray design” below) for 20 h at 65°C using a NimbleGen hybridization system 4 (NimbleGen/Roche) and scanned afterwards with an Agilent Technologies DNA microarray scanner G2565CA. cDNA preparation for RT-qPCR followed a different protocol.

Article Title: MicroRNA-214 promotes hepatic stellate cell activation and liver fibrosis by suppressing Sufu expression
Article Snippet: Microarray analysis Total RNAs were isolated from quiescent (cultured for 1 day) and activated (cultured for 12 days) primary HSCs, respectively, using TRIzol reagent (Life Technologies, Grand Island, NY, USA) and purified using mirVana™ miRNA Isolation Kit (Life Technologies, Grand Island, NY, USA). .. Hybridization signals were detected by DNA microarray scanner G2565CA (Agilent Technologies, Santa Clara, CA, USA), and the scanned images were analyzed using Agilent Feature Extraction software (version 10.7).

Labeling:

Article Title: Outer Membrane Vesicles of a Human Commensal Mediate Immune Regulation and Disease Protection
Article Snippet: RNA samples (1ug total RNA) from BMDCs were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent). .. Microarrays were analyzed using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1.

Article Title: Gene Expression Profiling in a Mouse Model Identifies Fetal Liver- and Placenta-Derived Potential Biomarkers for Down Syndrome Screening
Article Snippet: Afterwards, the slides were washed according to the Nimblegen Arrays User's Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). .. Each microarray corresponded to labeled RNA from one individual embryo.

Article Title: Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression
Article Snippet: For dual color hybridization of the Agilent chips miRNA samples from RAS transgenics were labeled with Hy3 and samples from control fish were labeled with Hy5 with miRCURYTM LNA microRNA, Hy3TM /Hy5TM Power Labeling kit (Exiqon) using 1 microgram of total RNA according to the manufacturer’s instructions. .. The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies.

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: The labeled cRNA samples were subsequently purified using RNeasy mini spin columns (Qiagen) according to the manufacturer’s protocol and the quantity was recorded using a NanoDrop spectrophotometer. .. Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent).

Article Title: A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis
Article Snippet: Total RNA (0.2 μg) was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies). .. The fluorescence signals were detected by an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 10.7.1.1 software.

Article Title: Germline TP53 mutations result into a constitutive defect of p53 DNA binding and transcriptional response to DNA damage
Article Snippet: Briefly, starting from 100 ng of total RNA,cRNA was synthesized and labelled using the low input Quick Amp Labeling Kit (Agilent), with Cy3 (for untreated cells) and Cy5 (for treated cells). .. Following co-hybridization, microarrays were scanned (DNA microarray scanner G2565CA, Agilent Technologies) with a resolution of 5 µm.

Article Title: Transcriptional repression of DNA repair genes is a hallmark and a cause of cellular senescence
Article Snippet: Briefly, cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies). .. Microarrays were washed and scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).

Article Title: Gene Expression Changes in the Olfactory Bulb of Mice Induced by Exposure to Diesel Exhaust Are Dependent on Animal Rearing Environment
Article Snippet: Each of the pooled RNA samples was labeled with Cy3 and hybridized to a SurePrint G3 Mouse GE 8×60K microarray (Agilent Technologies) consisting of 62,976 spots (28,620 genes) according to the protocol of DNA Chip Research Inc. (Kanagawa, Japan). .. After hybridization with fluorescent-labeled cDNA, the microarray was washed using Gene Expression Wash Buffers Pack (Agilent Technologies) and then scanned by a DNA microarray Scanner G2565CA (Agilent Technologies).

Article Title: MicroRNA-214 promotes hepatic stellate cell activation and liver fibrosis by suppressing Sufu expression
Article Snippet: The purified total RNAs were labeled and hybridized with microchip using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA, USA). .. Hybridization signals were detected by DNA microarray scanner G2565CA (Agilent Technologies, Santa Clara, CA, USA), and the scanned images were analyzed using Agilent Feature Extraction software (version 10.7).

Purification:

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: The labeled cRNA samples were subsequently purified using RNeasy mini spin columns (Qiagen) according to the manufacturer’s protocol and the quantity was recorded using a NanoDrop spectrophotometer. .. Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent).

Article Title: Transcriptional repression of DNA repair genes is a hallmark and a cause of cellular senescence
Article Snippet: Then, 1650 ng of Cy3-labeled cRNAs purified using the RNeasy Mini-spin columns (Qiagen) were hybridized on to the 4 × 44 K arrays for 17 h at 65 °C. .. Microarrays were washed and scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).

Article Title: MicroRNA-214 promotes hepatic stellate cell activation and liver fibrosis by suppressing Sufu expression
Article Snippet: The purified total RNAs were labeled and hybridized with microchip using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA, USA). .. Hybridization signals were detected by DNA microarray scanner G2565CA (Agilent Technologies, Santa Clara, CA, USA), and the scanned images were analyzed using Agilent Feature Extraction software (version 10.7).

Transgenic Assay:

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent). .. The qualified experiments were further processed; raw data (gene expression) was first quantile normalized and fold changes were calculated between transgenic and wild type samples for control and drought stress treatments.

Periodic Counter-current Chromatography:

Article Title: Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806
Article Snippet: .. MicroElute cleanup kit) and testing for Cy-dye incorporation efficiency (NanoDrop ND-1000; measurements were compared to those for control samples), Cy3- and Cy5-labeled cDNAs were hybridized to custom Microcystis sp. strain PCC 7806 microarrays (for array specifications, see “Microarray design” below) for 20 h at 65°C using a NimbleGen hybridization system 4 (NimbleGen/Roche) and scanned afterwards with an Agilent Technologies DNA microarray scanner G2565CA. cDNA preparation for RT-qPCR followed a different protocol. .. After DNA digestion and test PCRs, total RNA quality was checked by RNA agarose gel electrophoresis.

Chromatin Immunoprecipitation:

Article Title: Outer Membrane Vesicles of a Human Commensal Mediate Immune Regulation and Disease Protection
Article Snippet: Microarrays were analyzed using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1. .. Microarrays were analyzed using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1.

Article Title: Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806
Article Snippet: Following an RNA integrity check with an RNA 6000 Nano chip on a 2100 Bioanalyzer (Agilent Technologies), 3 to 5 μg of DNA-free total RNA samples for microarrays served as templates in random primed reverse transcription reactions (Superscript II RT; Life Technologies) incorporating Cy3- and Cy5-labeled dUTPs into cDNA products of control and treatment samples, respectively. .. MicroElute cleanup kit) and testing for Cy-dye incorporation efficiency (NanoDrop ND-1000; measurements were compared to those for control samples), Cy3- and Cy5-labeled cDNAs were hybridized to custom Microcystis sp. strain PCC 7806 microarrays (for array specifications, see “Microarray design” below) for 20 h at 65°C using a NimbleGen hybridization system 4 (NimbleGen/Roche) and scanned afterwards with an Agilent Technologies DNA microarray scanner G2565CA. cDNA preparation for RT-qPCR followed a different protocol.

Software:

Article Title: Outer Membrane Vesicles of a Human Commensal Mediate Immune Regulation and Disease Protection
Article Snippet: .. Microarrays were analyzed using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1. ..

Article Title: Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression
Article Snippet: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. .. Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies).

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent). .. The resultant microarray TIF images were processed to run batch extractions by choosing the appropriate grid using Agilent’s Feature Extraction Software version 11.0.

Article Title: A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis
Article Snippet: .. The fluorescence signals were detected by an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 10.7.1.1 software. .. Three biological repeats were conducted using cDNAs obtained from Ler and proatcape1 in 1/2 MS medium and with 12h of 125mM NaCl treatment.

Article Title: Germline TP53 mutations result into a constitutive defect of p53 DNA binding and transcriptional response to DNA damage
Article Snippet: Following co-hybridization, microarrays were scanned (DNA microarray scanner G2565CA, Agilent Technologies) with a resolution of 5 µm. .. GeneSpring GX 14.5 software (Agilent Technologies) was used to select the differentially expressed genes between treated and untreated cells in both replicates (Student t -test, P -value < 0.005).

Article Title: Transcriptional repression of DNA repair genes is a hallmark and a cause of cellular senescence
Article Snippet: Microarrays were washed and scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies). .. Fluorescent signals were extracted and normalized using the Feature Extraction Software Version 10.5.1.1 (Agilent Technologies), then transferred to the Genespring GX 12.6 software (Agilent Technologies) for data processing and data mining.

Article Title: Gene Expression Changes in the Olfactory Bulb of Mice Induced by Exposure to Diesel Exhaust Are Dependent on Animal Rearing Environment
Article Snippet: After hybridization with fluorescent-labeled cDNA, the microarray was washed using Gene Expression Wash Buffers Pack (Agilent Technologies) and then scanned by a DNA microarray Scanner G2565CA (Agilent Technologies). .. Scanner output images were normalized and digitalized by Agilent Feature Extraction software according to the Minimum Information about a Microarray Experiment guidelines and a pre-processing method for Agilent data .

Article Title: Changes in Bowel Microbiota Induced by Feeding Weanlings Resistant Starch Stimulate Transcriptomic and Physiological Responses
Article Snippet: .. The microarrays were scanned with an Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 9.0 Image Analysis software (Agilent Technologies). ..

Article Title: MicroRNA-214 promotes hepatic stellate cell activation and liver fibrosis by suppressing Sufu expression
Article Snippet: .. Hybridization signals were detected by DNA microarray scanner G2565CA (Agilent Technologies, Santa Clara, CA, USA), and the scanned images were analyzed using Agilent Feature Extraction software (version 10.7). .. Liver histopathology and fibrosis measurement Excised rat or mouse liver tissues were fixed in 4% paraformaldehyde, embedded in paraffin, and sectioned, followed by staining with H & E (Beyotime, Shanghai, China), trichrome (Masson) stain kit (Baso Diagnostics Inc., Zhuhai, China), or ORO staining (Beyotime, Shanghai, China).

Agarose Gel Electrophoresis:

Article Title: Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806
Article Snippet: MicroElute cleanup kit) and testing for Cy-dye incorporation efficiency (NanoDrop ND-1000; measurements were compared to those for control samples), Cy3- and Cy5-labeled cDNAs were hybridized to custom Microcystis sp. strain PCC 7806 microarrays (for array specifications, see “Microarray design” below) for 20 h at 65°C using a NimbleGen hybridization system 4 (NimbleGen/Roche) and scanned afterwards with an Agilent Technologies DNA microarray scanner G2565CA. cDNA preparation for RT-qPCR followed a different protocol. .. After DNA digestion and test PCRs, total RNA quality was checked by RNA agarose gel electrophoresis.

Spectrophotometry:

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: The labeled cRNA samples were subsequently purified using RNeasy mini spin columns (Qiagen) according to the manufacturer’s protocol and the quantity was recorded using a NanoDrop spectrophotometer. .. Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent).

Concentration Assay:

Article Title: Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
Article Snippet: RNA concentration was measured using a NanoDrop UV-VIS spectrophotometer (Peqlab) and quality of RNA samples was evaluated using RNA Nano 6000 kit (Agilent) and Bioanalyzer (Agilent). .. Hybridizations were carried out at 65 °C for 17 h. Slides were washed and scanned at high resolution of 2 microns using an Agilent DNA Microarray Scanner G2565CA (Agilent).

MicroChIP Assay:

Article Title: MicroRNA-214 promotes hepatic stellate cell activation and liver fibrosis by suppressing Sufu expression
Article Snippet: The purified total RNAs were labeled and hybridized with microchip using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA, USA). .. Hybridization signals were detected by DNA microarray scanner G2565CA (Agilent Technologies, Santa Clara, CA, USA), and the scanned images were analyzed using Agilent Feature Extraction software (version 10.7).

Fluorescence In Situ Hybridization:

Article Title: Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression
Article Snippet: For dual color hybridization of the Agilent chips miRNA samples from RAS transgenics were labeled with Hy3 and samples from control fish were labeled with Hy5 with miRCURYTM LNA microRNA, Hy3TM /Hy5TM Power Labeling kit (Exiqon) using 1 microgram of total RNA according to the manufacturer’s instructions. .. The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies.

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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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    94
    Agilent technologies dna microarray scanner g2565ba
    Cancer cell AGR2/CD10 RNA expression levels. Levels were determined through <t>DNA</t> <t>microarray</t> analysis with signal intensity values on the y -axis. Indicated on the x -axis are G3 and G4 primary tumor cell types, L luminal, LNCaP, C4-2, CL1, DU145, PC3 cell lines, LuCaP35, LuCaP 49 xenografts. Except for DU145 and LuCaP 49, the expression pattern is either CD10 or AGR2.
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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

    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

    Cancer cell AGR2/CD10 RNA expression levels. Levels were determined through DNA microarray analysis with signal intensity values on the y -axis. Indicated on the x -axis are G3 and G4 primary tumor cell types, L luminal, LNCaP, C4-2, CL1, DU145, PC3 cell lines, LuCaP35, LuCaP 49 xenografts. Except for DU145 and LuCaP 49, the expression pattern is either CD10 or AGR2.

    Journal: Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

    Article Title: Prostate cancer cell phenotypes based on AGR2 and CD10 expression

    doi: 10.1038/modpathol.2012.238

    Figure Lengend Snippet: Cancer cell AGR2/CD10 RNA expression levels. Levels were determined through DNA microarray analysis with signal intensity values on the y -axis. Indicated on the x -axis are G3 and G4 primary tumor cell types, L luminal, LNCaP, C4-2, CL1, DU145, PC3 cell lines, LuCaP35, LuCaP 49 xenografts. Except for DU145 and LuCaP 49, the expression pattern is either CD10 or AGR2.

    Article Snippet: Probe labeling and hybridization was performed following the Agilent protocol, and fluorescent array images were collected using the Agilent DNA microarray scanner G2565BA.

    Techniques: RNA Expression, Microarray, Expressing

    Expression levels of AGR2 and CD10 in xenografts. As inferred from DNA microarray analysis, these levels are presented in histogram format (top). CY3 intensity values are indicated on the y -axis. Because of the lower values for CD10, a separate histogram for CD10 is included (bottom). Note the ~6-fold decrease in CD10 from LuCaP 96 to Lu CaP 96CR.

    Journal: Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

    Article Title: Prostate cancer cell phenotypes based on AGR2 and CD10 expression

    doi: 10.1038/modpathol.2012.238

    Figure Lengend Snippet: Expression levels of AGR2 and CD10 in xenografts. As inferred from DNA microarray analysis, these levels are presented in histogram format (top). CY3 intensity values are indicated on the y -axis. Because of the lower values for CD10, a separate histogram for CD10 is included (bottom). Note the ~6-fold decrease in CD10 from LuCaP 96 to Lu CaP 96CR.

    Article Snippet: Probe labeling and hybridization was performed following the Agilent protocol, and fluorescent array images were collected using the Agilent DNA microarray scanner G2565BA.

    Techniques: Expressing, Microarray