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Agilent technologies color microarray
Overview of the workflow for <t>microarray</t> analysis. RNA is isolated from tissue samples (or cells) of interest. Quality of RNA is determined prior to proceeding with generation of cRNA, hybridization and data acquisition. Analysis of the microarray data is performed by the Agilent software. From there, the Gene Set Enrichment Analysis software is employed to yield genes that are significantly enriched in the assayed sample. Microarray data will also be used for Ingenuity Pathway Analysis (IPA) (and can be used for Gene Ontology [GO] analysis) to reveal pathways or biological processes that are enriched in the target sample.
Color Microarray, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Article Title: Microarray, IPA and GSEA Analysis in Mice Models

Journal: Bio-protocol

doi: 10.21769/BioProtoc.2999

Overview of the workflow for microarray analysis. RNA is isolated from tissue samples (or cells) of interest. Quality of RNA is determined prior to proceeding with generation of cRNA, hybridization and data acquisition. Analysis of the microarray data is performed by the Agilent software. From there, the Gene Set Enrichment Analysis software is employed to yield genes that are significantly enriched in the assayed sample. Microarray data will also be used for Ingenuity Pathway Analysis (IPA) (and can be used for Gene Ontology [GO] analysis) to reveal pathways or biological processes that are enriched in the target sample.
Figure Legend Snippet: Overview of the workflow for microarray analysis. RNA is isolated from tissue samples (or cells) of interest. Quality of RNA is determined prior to proceeding with generation of cRNA, hybridization and data acquisition. Analysis of the microarray data is performed by the Agilent software. From there, the Gene Set Enrichment Analysis software is employed to yield genes that are significantly enriched in the assayed sample. Microarray data will also be used for Ingenuity Pathway Analysis (IPA) (and can be used for Gene Ontology [GO] analysis) to reveal pathways or biological processes that are enriched in the target sample.

Techniques Used: Microarray, Isolation, Hybridization, Software, Indirect Immunoperoxidase Assay

Image of microarray wash dishes, SureHyb chamber and slide. A. Image of the wash dish with metal stir bar (left) and slide holder. B. Assembled SureHyb chamber, cover and clamp. C. Individual parts of the SureHyb assembly kit. Top is the chamber, the microarray slide sits on top of it and the cover (middle) is gently placed on top. The clamp (bottom) is then used to ensure the slide and chamber stay tightly together. D. Image of microarray slides, the visible barcodes clearly state “Agilent” and are to be used for proper orientation.
Figure Legend Snippet: Image of microarray wash dishes, SureHyb chamber and slide. A. Image of the wash dish with metal stir bar (left) and slide holder. B. Assembled SureHyb chamber, cover and clamp. C. Individual parts of the SureHyb assembly kit. Top is the chamber, the microarray slide sits on top of it and the cover (middle) is gently placed on top. The clamp (bottom) is then used to ensure the slide and chamber stay tightly together. D. Image of microarray slides, the visible barcodes clearly state “Agilent” and are to be used for proper orientation.

Techniques Used: Microarray

Related Articles

In Vivo:

Article Title: Establishing a hematopoietic genetic network through locus-specific integration of chromatin regulators
Article Snippet: Measurement of protein-DNA interactions in vivo by chromatin immunoprecipitation. .. EDGE(3): A web-based solution for management and analysis of Agilent two color microarray experiments.

Amplification:

Article Title: Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity
Article Snippet: .. Agilent one color microarray and expression analysis Total RNA was amplified by the WTA2 kit (Sigma-Aldrich, St. Louis, MO, USA), according to the manufacturer's protocol. cDNAs were chemically labeled with Kreatech ULS RNA Labeling Kit (Kreatech Diagnostics, Durham, NC, USA). .. Labeled cDNA was purified with Qiagen PCR purification columns, and cDNAs were quantitated on a NanoDrop spectrophotometer. cDNA samples were hybridized to Agilent Mouse_v1 8x60K microarrays (Design ID-028005, Agilent Technologies, Santa Clara, CA, USA).

Fluorescence:

Article Title: Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity
Article Snippet: Agilent one color microarray and expression analysis Total RNA was amplified by the WTA2 kit (Sigma-Aldrich, St. Louis, MO, USA), according to the manufacturer's protocol. cDNAs were chemically labeled with Kreatech ULS RNA Labeling Kit (Kreatech Diagnostics, Durham, NC, USA). .. Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to the manufacturer's specifications.

Isolation:

Article Title: Microarray, IPA and GSEA Analysis in Mice Models
Article Snippet: .. Equipment RNA isolation and cDNA synthesis Balance Pipettes (1,000 μl, 200 μl) Vortex (e.g ., Scientific Industries, model: Vortex-Genie 2, catalog number: SI0236) Centrifuge capable of reaching 16,000 × g and 4 °C for 1.5 ml tubes (Eppendorf, model: 5424 R) Tissue homogenizer (e.g ., Fisher Scientific, catalog number: FB120110) Heat block capable of maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 65 °C, 37 °C, 25 °C, 70 °C Water bath (e.g ., Thermo Fisher Scientific, catalog number: TSGP02) Optional: Rotating incubator Optional: Rotator rack Microarray Stir bar Pipettes (1,000 μl, 200 μl, 10 μl, multi-channel pipette) Centrifuge (Eppendorf, model: 5424) Agilent Technology Surescan Microarray Scanner Hybridization oven (Agilent Technologies, catalog number: G2545A) NanoDrop™ ND-1000 UV-VIS Spectrophotometer version 3.2.1 or higher (Thermo Fisher Scientific, model: NanoDrop™ 1000, catalog number: ND-1000) Heat block capable to maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 80 °C, 70 °C, 60 °C, 40 °C, 37 °C Agilent Gene Expression Two Color Microarray (Agilent Technologies, catalog number: G4140-90050) RNA quantification and quality control Nanodrop™ 2000c (or spectrophotometer) (Thermo Fisher Scientific, model: NanoDrop™ 2000c) Agilent Bioanalyzer 2100 qRT-PCR Roche Light Cycler 480 PCR System for 96-well plate .. Software SAS software for statistical analysis ( https://www.sas.com/en_us/software/universitv-edition.html ) OliqoAnalvzer 3.1 (IDT) ( https://www.idtdna.com/calc/analyzer ) GSEA (Gene set enrichment analysis) software available at: http://software.broadinstitute.org/gsea/index.jsp IPA (Ingenuity pathway analysis) software available at: https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ Agilent Microarray Scan Control (provided with current instrumentation) Agilent Feature Extraction Software 12.0 (provided with current instrumentation) Agilent GeneSpring GX software (provided with current instrumentation) NCBI Blastn ( https://blast.ncbi.nlm.nih.gov/Blast.cqi?PAGE_TYPE=BlastSearch ) UCSC Genome Browser, In silico PCR tool ( https://genome.ucsc.edu/ )

Article Title: Integrative Bioinformatics Analysis of Genomic and Proteomic Approaches to Understand the Transcriptional Regulatory Program in Coronary Artery Disease Pathways
Article Snippet: After isolation, RNA was cleaned up using RNeasy mini elute cleanup kit (Qiagen). .. The study design was formulated using one color microarray for cy3 using 8×60k slides from Agilent technologies.

Transferring:

Article Title: Microarray, IPA and GSEA Analysis in Mice Models
Article Snippet: .. Equipment RNA isolation and cDNA synthesis Balance Pipettes (1,000 μl, 200 μl) Vortex (e.g ., Scientific Industries, model: Vortex-Genie 2, catalog number: SI0236) Centrifuge capable of reaching 16,000 × g and 4 °C for 1.5 ml tubes (Eppendorf, model: 5424 R) Tissue homogenizer (e.g ., Fisher Scientific, catalog number: FB120110) Heat block capable of maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 65 °C, 37 °C, 25 °C, 70 °C Water bath (e.g ., Thermo Fisher Scientific, catalog number: TSGP02) Optional: Rotating incubator Optional: Rotator rack Microarray Stir bar Pipettes (1,000 μl, 200 μl, 10 μl, multi-channel pipette) Centrifuge (Eppendorf, model: 5424) Agilent Technology Surescan Microarray Scanner Hybridization oven (Agilent Technologies, catalog number: G2545A) NanoDrop™ ND-1000 UV-VIS Spectrophotometer version 3.2.1 or higher (Thermo Fisher Scientific, model: NanoDrop™ 1000, catalog number: ND-1000) Heat block capable to maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 80 °C, 70 °C, 60 °C, 40 °C, 37 °C Agilent Gene Expression Two Color Microarray (Agilent Technologies, catalog number: G4140-90050) RNA quantification and quality control Nanodrop™ 2000c (or spectrophotometer) (Thermo Fisher Scientific, model: NanoDrop™ 2000c) Agilent Bioanalyzer 2100 qRT-PCR Roche Light Cycler 480 PCR System for 96-well plate .. Software SAS software for statistical analysis ( https://www.sas.com/en_us/software/universitv-edition.html ) OliqoAnalvzer 3.1 (IDT) ( https://www.idtdna.com/calc/analyzer ) GSEA (Gene set enrichment analysis) software available at: http://software.broadinstitute.org/gsea/index.jsp IPA (Ingenuity pathway analysis) software available at: https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ Agilent Microarray Scan Control (provided with current instrumentation) Agilent Feature Extraction Software 12.0 (provided with current instrumentation) Agilent GeneSpring GX software (provided with current instrumentation) NCBI Blastn ( https://blast.ncbi.nlm.nih.gov/Blast.cqi?PAGE_TYPE=BlastSearch ) UCSC Genome Browser, In silico PCR tool ( https://genome.ucsc.edu/ )

Spectrophotometry:

Article Title: Microarray, IPA and GSEA Analysis in Mice Models
Article Snippet: .. Equipment RNA isolation and cDNA synthesis Balance Pipettes (1,000 μl, 200 μl) Vortex (e.g ., Scientific Industries, model: Vortex-Genie 2, catalog number: SI0236) Centrifuge capable of reaching 16,000 × g and 4 °C for 1.5 ml tubes (Eppendorf, model: 5424 R) Tissue homogenizer (e.g ., Fisher Scientific, catalog number: FB120110) Heat block capable of maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 65 °C, 37 °C, 25 °C, 70 °C Water bath (e.g ., Thermo Fisher Scientific, catalog number: TSGP02) Optional: Rotating incubator Optional: Rotator rack Microarray Stir bar Pipettes (1,000 μl, 200 μl, 10 μl, multi-channel pipette) Centrifuge (Eppendorf, model: 5424) Agilent Technology Surescan Microarray Scanner Hybridization oven (Agilent Technologies, catalog number: G2545A) NanoDrop™ ND-1000 UV-VIS Spectrophotometer version 3.2.1 or higher (Thermo Fisher Scientific, model: NanoDrop™ 1000, catalog number: ND-1000) Heat block capable to maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 80 °C, 70 °C, 60 °C, 40 °C, 37 °C Agilent Gene Expression Two Color Microarray (Agilent Technologies, catalog number: G4140-90050) RNA quantification and quality control Nanodrop™ 2000c (or spectrophotometer) (Thermo Fisher Scientific, model: NanoDrop™ 2000c) Agilent Bioanalyzer 2100 qRT-PCR Roche Light Cycler 480 PCR System for 96-well plate .. Software SAS software for statistical analysis ( https://www.sas.com/en_us/software/universitv-edition.html ) OliqoAnalvzer 3.1 (IDT) ( https://www.idtdna.com/calc/analyzer ) GSEA (Gene set enrichment analysis) software available at: http://software.broadinstitute.org/gsea/index.jsp IPA (Ingenuity pathway analysis) software available at: https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ Agilent Microarray Scan Control (provided with current instrumentation) Agilent Feature Extraction Software 12.0 (provided with current instrumentation) Agilent GeneSpring GX software (provided with current instrumentation) NCBI Blastn ( https://blast.ncbi.nlm.nih.gov/Blast.cqi?PAGE_TYPE=BlastSearch ) UCSC Genome Browser, In silico PCR tool ( https://genome.ucsc.edu/ )

Article Title: Integrative Bioinformatics Analysis of Genomic and Proteomic Approaches to Understand the Transcriptional Regulatory Program in Coronary Artery Disease Pathways
Article Snippet: The RNA quantity and quality were determined by NanoDrop ND-1000 UV-VIS Spectrophotometer and Agilent Bioanalyzer 2100 (Agilent Technologies). .. The study design was formulated using one color microarray for cy3 using 8×60k slides from Agilent technologies.

Article Title: Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity
Article Snippet: Agilent one color microarray and expression analysis Total RNA was amplified by the WTA2 kit (Sigma-Aldrich, St. Louis, MO, USA), according to the manufacturer's protocol. cDNAs were chemically labeled with Kreatech ULS RNA Labeling Kit (Kreatech Diagnostics, Durham, NC, USA). .. Labeled cDNA was purified with Qiagen PCR purification columns, and cDNAs were quantitated on a NanoDrop spectrophotometer. cDNA samples were hybridized to Agilent Mouse_v1 8x60K microarrays (Design ID-028005, Agilent Technologies, Santa Clara, CA, USA).

Purification:

Article Title: Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity
Article Snippet: Agilent one color microarray and expression analysis Total RNA was amplified by the WTA2 kit (Sigma-Aldrich, St. Louis, MO, USA), according to the manufacturer's protocol. cDNAs were chemically labeled with Kreatech ULS RNA Labeling Kit (Kreatech Diagnostics, Durham, NC, USA). .. Labeled cDNA was purified with Qiagen PCR purification columns, and cDNAs were quantitated on a NanoDrop spectrophotometer. cDNA samples were hybridized to Agilent Mouse_v1 8x60K microarrays (Design ID-028005, Agilent Technologies, Santa Clara, CA, USA).

Labeling:

Article Title: Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity
Article Snippet: .. Agilent one color microarray and expression analysis Total RNA was amplified by the WTA2 kit (Sigma-Aldrich, St. Louis, MO, USA), according to the manufacturer's protocol. cDNAs were chemically labeled with Kreatech ULS RNA Labeling Kit (Kreatech Diagnostics, Durham, NC, USA). .. Labeled cDNA was purified with Qiagen PCR purification columns, and cDNAs were quantitated on a NanoDrop spectrophotometer. cDNA samples were hybridized to Agilent Mouse_v1 8x60K microarrays (Design ID-028005, Agilent Technologies, Santa Clara, CA, USA).

Microarray:

Article Title: Microarray, IPA and GSEA Analysis in Mice Models
Article Snippet: .. Equipment RNA isolation and cDNA synthesis Balance Pipettes (1,000 μl, 200 μl) Vortex (e.g ., Scientific Industries, model: Vortex-Genie 2, catalog number: SI0236) Centrifuge capable of reaching 16,000 × g and 4 °C for 1.5 ml tubes (Eppendorf, model: 5424 R) Tissue homogenizer (e.g ., Fisher Scientific, catalog number: FB120110) Heat block capable of maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 65 °C, 37 °C, 25 °C, 70 °C Water bath (e.g ., Thermo Fisher Scientific, catalog number: TSGP02) Optional: Rotating incubator Optional: Rotator rack Microarray Stir bar Pipettes (1,000 μl, 200 μl, 10 μl, multi-channel pipette) Centrifuge (Eppendorf, model: 5424) Agilent Technology Surescan Microarray Scanner Hybridization oven (Agilent Technologies, catalog number: G2545A) NanoDrop™ ND-1000 UV-VIS Spectrophotometer version 3.2.1 or higher (Thermo Fisher Scientific, model: NanoDrop™ 1000, catalog number: ND-1000) Heat block capable to maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 80 °C, 70 °C, 60 °C, 40 °C, 37 °C Agilent Gene Expression Two Color Microarray (Agilent Technologies, catalog number: G4140-90050) RNA quantification and quality control Nanodrop™ 2000c (or spectrophotometer) (Thermo Fisher Scientific, model: NanoDrop™ 2000c) Agilent Bioanalyzer 2100 qRT-PCR Roche Light Cycler 480 PCR System for 96-well plate .. Software SAS software for statistical analysis ( https://www.sas.com/en_us/software/universitv-edition.html ) OliqoAnalvzer 3.1 (IDT) ( https://www.idtdna.com/calc/analyzer ) GSEA (Gene set enrichment analysis) software available at: http://software.broadinstitute.org/gsea/index.jsp IPA (Ingenuity pathway analysis) software available at: https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ Agilent Microarray Scan Control (provided with current instrumentation) Agilent Feature Extraction Software 12.0 (provided with current instrumentation) Agilent GeneSpring GX software (provided with current instrumentation) NCBI Blastn ( https://blast.ncbi.nlm.nih.gov/Blast.cqi?PAGE_TYPE=BlastSearch ) UCSC Genome Browser, In silico PCR tool ( https://genome.ucsc.edu/ )

Article Title: Integrative Bioinformatics Analysis of Genomic and Proteomic Approaches to Understand the Transcriptional Regulatory Program in Coronary Artery Disease Pathways
Article Snippet: .. The study design was formulated using one color microarray for cy3 using 8×60k slides from Agilent technologies. .. Sample preparation One color spike mix was prepared and 2 ul of this mix was added to 50 ng (1.5 ul) of each RNA sample individually.

Article Title: The exosome complex establishes a barricade to erythroid maturation
Article Snippet: .. EDGE(3): a web-based solution for management and analysis of Agilent two color microarray experiments. ..

Article Title: Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity
Article Snippet: .. Agilent one color microarray and expression analysis Total RNA was amplified by the WTA2 kit (Sigma-Aldrich, St. Louis, MO, USA), according to the manufacturer's protocol. cDNAs were chemically labeled with Kreatech ULS RNA Labeling Kit (Kreatech Diagnostics, Durham, NC, USA). .. Labeled cDNA was purified with Qiagen PCR purification columns, and cDNAs were quantitated on a NanoDrop spectrophotometer. cDNA samples were hybridized to Agilent Mouse_v1 8x60K microarrays (Design ID-028005, Agilent Technologies, Santa Clara, CA, USA).

Article Title: Cytochrome P450 1B1: An Unexpected Modulator of Liver Fatty Acid Homeostasis
Article Snippet: .. EDGE3 : A web-based solution for management and analysis of Agilent two color microarray experiments. ..

Article Title: Establishing a hematopoietic genetic network through locus-specific integration of chromatin regulators
Article Snippet: .. EDGE(3): A web-based solution for management and analysis of Agilent two color microarray experiments. ..

Article Title: Gene Expression Analysis Reveals the Concurrent Activation of Proapoptotic and Antioxidant-Defensive Mechanisms in Flavokawain B–Treated Cervical Cancer HeLa Cells
Article Snippet: .. Gene Expression Profiling Using Microarray Differential gene expression of untreated HeLa cells and HeLa cells treated with FKB for 48 hours was assayed by Agilent one color microarray using a human gene expression v2 microarray chip (Agilent Technologies, USA). .. In brief, RNA was extracted from control and FKB-treated HeLa cells by Qiagen RNeasy plus mini kit (Qiagen, USA).

Article Title: Diet-dependent retinoid effects on liver gene expression include stellate and inflammation markers and parallel effects of the nuclear repressor, Shp
Article Snippet: .. EDGE(3): a web-based solution for management and analysis of Agilent two color microarray experiments. ..

Imaging:

Article Title: Cytochrome P450 1B1: An Unexpected Modulator of Liver Fatty Acid Homeostasis
Article Snippet: J Magn Reson Imaging. .. EDGE3 : A web-based solution for management and analysis of Agilent two color microarray experiments.

Expressing:

Article Title: Microarray, IPA and GSEA Analysis in Mice Models
Article Snippet: .. Equipment RNA isolation and cDNA synthesis Balance Pipettes (1,000 μl, 200 μl) Vortex (e.g ., Scientific Industries, model: Vortex-Genie 2, catalog number: SI0236) Centrifuge capable of reaching 16,000 × g and 4 °C for 1.5 ml tubes (Eppendorf, model: 5424 R) Tissue homogenizer (e.g ., Fisher Scientific, catalog number: FB120110) Heat block capable of maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 65 °C, 37 °C, 25 °C, 70 °C Water bath (e.g ., Thermo Fisher Scientific, catalog number: TSGP02) Optional: Rotating incubator Optional: Rotator rack Microarray Stir bar Pipettes (1,000 μl, 200 μl, 10 μl, multi-channel pipette) Centrifuge (Eppendorf, model: 5424) Agilent Technology Surescan Microarray Scanner Hybridization oven (Agilent Technologies, catalog number: G2545A) NanoDrop™ ND-1000 UV-VIS Spectrophotometer version 3.2.1 or higher (Thermo Fisher Scientific, model: NanoDrop™ 1000, catalog number: ND-1000) Heat block capable to maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 80 °C, 70 °C, 60 °C, 40 °C, 37 °C Agilent Gene Expression Two Color Microarray (Agilent Technologies, catalog number: G4140-90050) RNA quantification and quality control Nanodrop™ 2000c (or spectrophotometer) (Thermo Fisher Scientific, model: NanoDrop™ 2000c) Agilent Bioanalyzer 2100 qRT-PCR Roche Light Cycler 480 PCR System for 96-well plate .. Software SAS software for statistical analysis ( https://www.sas.com/en_us/software/universitv-edition.html ) OliqoAnalvzer 3.1 (IDT) ( https://www.idtdna.com/calc/analyzer ) GSEA (Gene set enrichment analysis) software available at: http://software.broadinstitute.org/gsea/index.jsp IPA (Ingenuity pathway analysis) software available at: https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ Agilent Microarray Scan Control (provided with current instrumentation) Agilent Feature Extraction Software 12.0 (provided with current instrumentation) Agilent GeneSpring GX software (provided with current instrumentation) NCBI Blastn ( https://blast.ncbi.nlm.nih.gov/Blast.cqi?PAGE_TYPE=BlastSearch ) UCSC Genome Browser, In silico PCR tool ( https://genome.ucsc.edu/ )

Article Title: Integrative Bioinformatics Analysis of Genomic and Proteomic Approaches to Understand the Transcriptional Regulatory Program in Coronary Artery Disease Pathways
Article Snippet: Paragraph title: Gene Expression Studies ... The study design was formulated using one color microarray for cy3 using 8×60k slides from Agilent technologies.

Article Title: Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity
Article Snippet: .. Agilent one color microarray and expression analysis Total RNA was amplified by the WTA2 kit (Sigma-Aldrich, St. Louis, MO, USA), according to the manufacturer's protocol. cDNAs were chemically labeled with Kreatech ULS RNA Labeling Kit (Kreatech Diagnostics, Durham, NC, USA). .. Labeled cDNA was purified with Qiagen PCR purification columns, and cDNAs were quantitated on a NanoDrop spectrophotometer. cDNA samples were hybridized to Agilent Mouse_v1 8x60K microarrays (Design ID-028005, Agilent Technologies, Santa Clara, CA, USA).

Article Title: Gene Expression Analysis Reveals the Concurrent Activation of Proapoptotic and Antioxidant-Defensive Mechanisms in Flavokawain B–Treated Cervical Cancer HeLa Cells
Article Snippet: .. Gene Expression Profiling Using Microarray Differential gene expression of untreated HeLa cells and HeLa cells treated with FKB for 48 hours was assayed by Agilent one color microarray using a human gene expression v2 microarray chip (Agilent Technologies, USA). .. In brief, RNA was extracted from control and FKB-treated HeLa cells by Qiagen RNeasy plus mini kit (Qiagen, USA).

Genome Wide:

Article Title: The exosome complex establishes a barricade to erythroid maturation
Article Snippet: Fujiwara T, O’Geen H, Keles S, et al. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. .. EDGE(3): a web-based solution for management and analysis of Agilent two color microarray experiments.

Polymerase Chain Reaction:

Article Title: Microarray, IPA and GSEA Analysis in Mice Models
Article Snippet: .. Equipment RNA isolation and cDNA synthesis Balance Pipettes (1,000 μl, 200 μl) Vortex (e.g ., Scientific Industries, model: Vortex-Genie 2, catalog number: SI0236) Centrifuge capable of reaching 16,000 × g and 4 °C for 1.5 ml tubes (Eppendorf, model: 5424 R) Tissue homogenizer (e.g ., Fisher Scientific, catalog number: FB120110) Heat block capable of maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 65 °C, 37 °C, 25 °C, 70 °C Water bath (e.g ., Thermo Fisher Scientific, catalog number: TSGP02) Optional: Rotating incubator Optional: Rotator rack Microarray Stir bar Pipettes (1,000 μl, 200 μl, 10 μl, multi-channel pipette) Centrifuge (Eppendorf, model: 5424) Agilent Technology Surescan Microarray Scanner Hybridization oven (Agilent Technologies, catalog number: G2545A) NanoDrop™ ND-1000 UV-VIS Spectrophotometer version 3.2.1 or higher (Thermo Fisher Scientific, model: NanoDrop™ 1000, catalog number: ND-1000) Heat block capable to maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 80 °C, 70 °C, 60 °C, 40 °C, 37 °C Agilent Gene Expression Two Color Microarray (Agilent Technologies, catalog number: G4140-90050) RNA quantification and quality control Nanodrop™ 2000c (or spectrophotometer) (Thermo Fisher Scientific, model: NanoDrop™ 2000c) Agilent Bioanalyzer 2100 qRT-PCR Roche Light Cycler 480 PCR System for 96-well plate .. Software SAS software for statistical analysis ( https://www.sas.com/en_us/software/universitv-edition.html ) OliqoAnalvzer 3.1 (IDT) ( https://www.idtdna.com/calc/analyzer ) GSEA (Gene set enrichment analysis) software available at: http://software.broadinstitute.org/gsea/index.jsp IPA (Ingenuity pathway analysis) software available at: https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ Agilent Microarray Scan Control (provided with current instrumentation) Agilent Feature Extraction Software 12.0 (provided with current instrumentation) Agilent GeneSpring GX software (provided with current instrumentation) NCBI Blastn ( https://blast.ncbi.nlm.nih.gov/Blast.cqi?PAGE_TYPE=BlastSearch ) UCSC Genome Browser, In silico PCR tool ( https://genome.ucsc.edu/ )

Article Title: Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity
Article Snippet: Agilent one color microarray and expression analysis Total RNA was amplified by the WTA2 kit (Sigma-Aldrich, St. Louis, MO, USA), according to the manufacturer's protocol. cDNAs were chemically labeled with Kreatech ULS RNA Labeling Kit (Kreatech Diagnostics, Durham, NC, USA). .. Labeled cDNA was purified with Qiagen PCR purification columns, and cDNAs were quantitated on a NanoDrop spectrophotometer. cDNA samples were hybridized to Agilent Mouse_v1 8x60K microarrays (Design ID-028005, Agilent Technologies, Santa Clara, CA, USA).

Quantitative RT-PCR:

Article Title: Microarray, IPA and GSEA Analysis in Mice Models
Article Snippet: .. Equipment RNA isolation and cDNA synthesis Balance Pipettes (1,000 μl, 200 μl) Vortex (e.g ., Scientific Industries, model: Vortex-Genie 2, catalog number: SI0236) Centrifuge capable of reaching 16,000 × g and 4 °C for 1.5 ml tubes (Eppendorf, model: 5424 R) Tissue homogenizer (e.g ., Fisher Scientific, catalog number: FB120110) Heat block capable of maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 65 °C, 37 °C, 25 °C, 70 °C Water bath (e.g ., Thermo Fisher Scientific, catalog number: TSGP02) Optional: Rotating incubator Optional: Rotator rack Microarray Stir bar Pipettes (1,000 μl, 200 μl, 10 μl, multi-channel pipette) Centrifuge (Eppendorf, model: 5424) Agilent Technology Surescan Microarray Scanner Hybridization oven (Agilent Technologies, catalog number: G2545A) NanoDrop™ ND-1000 UV-VIS Spectrophotometer version 3.2.1 or higher (Thermo Fisher Scientific, model: NanoDrop™ 1000, catalog number: ND-1000) Heat block capable to maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 80 °C, 70 °C, 60 °C, 40 °C, 37 °C Agilent Gene Expression Two Color Microarray (Agilent Technologies, catalog number: G4140-90050) RNA quantification and quality control Nanodrop™ 2000c (or spectrophotometer) (Thermo Fisher Scientific, model: NanoDrop™ 2000c) Agilent Bioanalyzer 2100 qRT-PCR Roche Light Cycler 480 PCR System for 96-well plate .. Software SAS software for statistical analysis ( https://www.sas.com/en_us/software/universitv-edition.html ) OliqoAnalvzer 3.1 (IDT) ( https://www.idtdna.com/calc/analyzer ) GSEA (Gene set enrichment analysis) software available at: http://software.broadinstitute.org/gsea/index.jsp IPA (Ingenuity pathway analysis) software available at: https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ Agilent Microarray Scan Control (provided with current instrumentation) Agilent Feature Extraction Software 12.0 (provided with current instrumentation) Agilent GeneSpring GX software (provided with current instrumentation) NCBI Blastn ( https://blast.ncbi.nlm.nih.gov/Blast.cqi?PAGE_TYPE=BlastSearch ) UCSC Genome Browser, In silico PCR tool ( https://genome.ucsc.edu/ )

Hybridization:

Article Title: Microarray, IPA and GSEA Analysis in Mice Models
Article Snippet: .. Equipment RNA isolation and cDNA synthesis Balance Pipettes (1,000 μl, 200 μl) Vortex (e.g ., Scientific Industries, model: Vortex-Genie 2, catalog number: SI0236) Centrifuge capable of reaching 16,000 × g and 4 °C for 1.5 ml tubes (Eppendorf, model: 5424 R) Tissue homogenizer (e.g ., Fisher Scientific, catalog number: FB120110) Heat block capable of maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 65 °C, 37 °C, 25 °C, 70 °C Water bath (e.g ., Thermo Fisher Scientific, catalog number: TSGP02) Optional: Rotating incubator Optional: Rotator rack Microarray Stir bar Pipettes (1,000 μl, 200 μl, 10 μl, multi-channel pipette) Centrifuge (Eppendorf, model: 5424) Agilent Technology Surescan Microarray Scanner Hybridization oven (Agilent Technologies, catalog number: G2545A) NanoDrop™ ND-1000 UV-VIS Spectrophotometer version 3.2.1 or higher (Thermo Fisher Scientific, model: NanoDrop™ 1000, catalog number: ND-1000) Heat block capable to maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 80 °C, 70 °C, 60 °C, 40 °C, 37 °C Agilent Gene Expression Two Color Microarray (Agilent Technologies, catalog number: G4140-90050) RNA quantification and quality control Nanodrop™ 2000c (or spectrophotometer) (Thermo Fisher Scientific, model: NanoDrop™ 2000c) Agilent Bioanalyzer 2100 qRT-PCR Roche Light Cycler 480 PCR System for 96-well plate .. Software SAS software for statistical analysis ( https://www.sas.com/en_us/software/universitv-edition.html ) OliqoAnalvzer 3.1 (IDT) ( https://www.idtdna.com/calc/analyzer ) GSEA (Gene set enrichment analysis) software available at: http://software.broadinstitute.org/gsea/index.jsp IPA (Ingenuity pathway analysis) software available at: https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ Agilent Microarray Scan Control (provided with current instrumentation) Agilent Feature Extraction Software 12.0 (provided with current instrumentation) Agilent GeneSpring GX software (provided with current instrumentation) NCBI Blastn ( https://blast.ncbi.nlm.nih.gov/Blast.cqi?PAGE_TYPE=BlastSearch ) UCSC Genome Browser, In silico PCR tool ( https://genome.ucsc.edu/ )

Chromatin Immunoprecipitation:

Article Title: Establishing a hematopoietic genetic network through locus-specific integration of chromatin regulators
Article Snippet: Measurement of protein-DNA interactions in vivo by chromatin immunoprecipitation. .. EDGE(3): A web-based solution for management and analysis of Agilent two color microarray experiments.

Article Title: Gene Expression Analysis Reveals the Concurrent Activation of Proapoptotic and Antioxidant-Defensive Mechanisms in Flavokawain B–Treated Cervical Cancer HeLa Cells
Article Snippet: .. Gene Expression Profiling Using Microarray Differential gene expression of untreated HeLa cells and HeLa cells treated with FKB for 48 hours was assayed by Agilent one color microarray using a human gene expression v2 microarray chip (Agilent Technologies, USA). .. In brief, RNA was extracted from control and FKB-treated HeLa cells by Qiagen RNeasy plus mini kit (Qiagen, USA).

Magnetic Resonance Imaging:

Article Title: Cytochrome P450 1B1: An Unexpected Modulator of Liver Fatty Acid Homeostasis
Article Snippet: Variations in T2* and fat content of murine brown and white adipose tissues by chemical-shift MRI. .. EDGE3 : A web-based solution for management and analysis of Agilent two color microarray experiments.

Blocking Assay:

Article Title: Microarray, IPA and GSEA Analysis in Mice Models
Article Snippet: .. Equipment RNA isolation and cDNA synthesis Balance Pipettes (1,000 μl, 200 μl) Vortex (e.g ., Scientific Industries, model: Vortex-Genie 2, catalog number: SI0236) Centrifuge capable of reaching 16,000 × g and 4 °C for 1.5 ml tubes (Eppendorf, model: 5424 R) Tissue homogenizer (e.g ., Fisher Scientific, catalog number: FB120110) Heat block capable of maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 65 °C, 37 °C, 25 °C, 70 °C Water bath (e.g ., Thermo Fisher Scientific, catalog number: TSGP02) Optional: Rotating incubator Optional: Rotator rack Microarray Stir bar Pipettes (1,000 μl, 200 μl, 10 μl, multi-channel pipette) Centrifuge (Eppendorf, model: 5424) Agilent Technology Surescan Microarray Scanner Hybridization oven (Agilent Technologies, catalog number: G2545A) NanoDrop™ ND-1000 UV-VIS Spectrophotometer version 3.2.1 or higher (Thermo Fisher Scientific, model: NanoDrop™ 1000, catalog number: ND-1000) Heat block capable to maintaining following temperatures for 1.7 ml micro-centrifuge tubes: 80 °C, 70 °C, 60 °C, 40 °C, 37 °C Agilent Gene Expression Two Color Microarray (Agilent Technologies, catalog number: G4140-90050) RNA quantification and quality control Nanodrop™ 2000c (or spectrophotometer) (Thermo Fisher Scientific, model: NanoDrop™ 2000c) Agilent Bioanalyzer 2100 qRT-PCR Roche Light Cycler 480 PCR System for 96-well plate .. Software SAS software for statistical analysis ( https://www.sas.com/en_us/software/universitv-edition.html ) OliqoAnalvzer 3.1 (IDT) ( https://www.idtdna.com/calc/analyzer ) GSEA (Gene set enrichment analysis) software available at: http://software.broadinstitute.org/gsea/index.jsp IPA (Ingenuity pathway analysis) software available at: https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ Agilent Microarray Scan Control (provided with current instrumentation) Agilent Feature Extraction Software 12.0 (provided with current instrumentation) Agilent GeneSpring GX software (provided with current instrumentation) NCBI Blastn ( https://blast.ncbi.nlm.nih.gov/Blast.cqi?PAGE_TYPE=BlastSearch ) UCSC Genome Browser, In silico PCR tool ( https://genome.ucsc.edu/ )

Software:

Article Title: Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity
Article Snippet: Agilent one color microarray and expression analysis Total RNA was amplified by the WTA2 kit (Sigma-Aldrich, St. Louis, MO, USA), according to the manufacturer's protocol. cDNAs were chemically labeled with Kreatech ULS RNA Labeling Kit (Kreatech Diagnostics, Durham, NC, USA). .. Gridding and analysis of images was performed using Feature Extraction software (v11.5.1.1, Agilent Technologies, Santa Clara, CA, USA).

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    Agilent technologies 2000c agilent bioanalyzer 2100 qrt pcr roche light cycler 480 pcr system
    2000c Agilent Bioanalyzer 2100 Qrt Pcr Roche Light Cycler 480 Pcr System, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 95/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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