The hybridization images were captured with GenePix 4000B (Axon Instruments, Terumo, CA, USA) and digitized by GenePix Pro 6.0 program (Axon Instruments). The average fluorescence intensity of each spot was calculated, and the local background was subtracted. All data normalization and the selection of the genes showing fold changes were performed with GeneSpring GX 7.3.1 (Silicon Genetics, Redwood City, CA, USA). The identified genes were filtered with a cut-off value based on the two-component error model after intensity-dependent normalization (LOWESS). The averages of the normalized ratio were calculated as the ratio of mean normalized signal channel intensity to mean normalized control channel intensity.
Genepix pro 6.0 program
Manufactured by Molecular Devices
Sourced in United States
The GenePix Pro 6.0 program is a software tool designed for the analysis and processing of microarray data. It provides users with a suite of tools for image analysis, data extraction, and visualization of microarray experiment results.
Automatically generated - may contain errors
Lab products found in correlation
Axon genepix 4000b microarray scanner, by Molecular Devices (4 mentions)
Mircury lna array, by Qiagen (3 mentions)
Mirneasy isolation kit, by Qiagen (2 mentions)
Nanodrop nd 1000 spectrophotometry, by Thermo Fisher Scientific (2 mentions)
Genespring gx version 7, by Agilent Technologies (2 mentions)
Trizol, by Thermo Fisher Scientific (2 mentions)
Genepix 4000b, by Molecular Devices (1 mentions)
Purelink mirna isolation kit, by Thermo Fisher Scientific (1 mentions)
Mircury hy3 hy5 power labeling kit, by Qiagen (1 mentions)
Genespring gx software version 7, by Agilent Technologies (1 mentions)
Agilent s 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Mirnaeasy mini kit, by Qiagen (1 mentions)
5 protocols using genepix pro 6.0 program
1
Gene Expression Analysis Workflow
2
Differential miRNA Expression in Osteoarthritis
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Total RNA was extracted from the articular cartilage tissues of control and OA rats using TRIzol (ThermoFisher 15596026, USA) and PureLink™ miRNA Isolation Kit (ThermoFisher K157001) according to manufacturer's instructions. The quantity and quality of the RNA was then measured using a NanoDrop 1000 spectrophotometer (Youpu, China). The samples were labeled with a fluorescent dye (miRCURY™Hy3™/Hy5™ Power labeling kit) and hybridized to a miRCURY LNA array (Exiqon, Denmark). After washing, the array was scanned using an Axon GenePix 4000 B microarray scanner (Axon Instruments, USA), and the data was analyzed using the GenePix Pro 6.0 program (Axon Instruments). Data were normalized by median normalization. After normalization, the miRNAs that were significantly differentially expressed between the control and OA groups were identified by Volcano Plot filtering (Origin 2021, USA).
3
Differential miRNA Expression in Endometriosis
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Total RNA was extracted from three eutopic and three ectopic endometrium tissues by miRNeasy isolation kit (Qiagen, Inc.) according to the manufacturer's protocol. Total RNA (200 ng) was labeled with fluorescence dye Hy3 or Hy5 using the miRCURY Hy3/Hy5 Power Labeling kit (Exiqon). After hybridization on the miRCURY™ LNA Array (v.18.0, Exiqon), data obtained from Axon GenePix 4000B microarray scanner (Axon Instruments; Molecular Devices, LLC) were imported into the GenePix Pro 6.0 program (Axon Instruments; Molecular Devices, LLC) for analysis (15 (link)). The bioinformatics analysis was performed by RiboBio Co., Ltd. Finally, the heatmap of miRNAs with the most marked differences was created using hierarchical clustering in GeneSpring GX software, version 7.3 (Agilent Technologies, Inc.).
4
Profiling Circulating miRNAs in Cerebral Ischemia
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Total RNA was isolated from the sera of patients with cerebral ischemia by a miRNAeasy mini kit (Qiagen, Inc., Valencia, CA, USA). The purity and quantity of total RNA were evaluated by NanoDrop ND-1000 Spectrophotometry (Thermo Fisher Scientific, Inc., Waltham, MA, USA) and Agilent's 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). Total RNA (200 ng) was labeled and hybridized with the miRCURY™ LNA Array (version 16.0; Exiqon; Qiagen, Inc.). Following washing, Axon GenePix 4000B microarray scanner (Axon Instruments; Molecular Devices, LLC, Sunnyvale, CA, USA) was used to scan the fluorescence intensity of the microarray. Scanned images were then imported into the GenePix Pro6.0 program (Axon Instruments; Molecular Devices, LLC) for grid alignment and data extraction. Finally, the heat map of the 57 miRNAs with the most evident differences was created using a method of hierarchical clustering with GeneSpring GX, version 7.3 (Agilent Technologies, Inc.).
5
Profiling Differential miRNA Expression in Diabetic Nephropathy
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Total RNA was isolated from three peripheral blood samples from patients with DN and three peripheral blood samples from healthy controls by miRNeasy isolation kit (Qiagen, Milan, Italy) according to the manufacturer’s protocol. The RNA quantity was assessed by NanoDrop ND-1000 spectrophotometry (Thermo Fisher Scientific, Inc., Waltham, MA, U.S.A.). Total RNA (200 ng) was labeled using the miRCURY Hy3/Hy5 Power Labeling kit and hybridized on the miRCURY™ LNA array (v.16.0; Exiqon A/S, Copenhagen, Denmark) according to the manufacturer’s protocol. Scanned images from Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, U.S.A.) were imported into the GenePix Pro6.0 program (Axon Instruments) for grid alignment and data extraction. The miRNAs with intensities ≥50 were used to calculate a normalization factor in all samples. The heatmap of the 50 miRNAs with the most marked differences was created using a method of hierarchical clustering by GeneSpring GX, version 7.3 (Agilent Technologies, Inc.).
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