Genespring 12.6.1 platform

Manufactured by Agilent Technologies

Sourced in United States

GeneSpring 12.6.1 is a bioinformatics software platform designed for the analysis and visualization of genomic data. It provides a comprehensive suite of tools for data import, quality control, gene expression analysis, pathway analysis, and data visualization.

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Lab products found in correlation

Genespring gx software, by Agilent Technologies (2 mentions) Genechip mirna 2.0 array, by Thermo Fisher Scientific (1 mentions) Microarray suite 5, by Thermo Fisher Scientific (1 mentions) Flashtag biotin hsr rna labeling kit, by Thermo Fisher Scientific (1 mentions) Genearray scanner 3000 7g, by Agilent Technologies (1 mentions)

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GeneSpring (227 citations) GeneSpring 12.0 (79 citations)

2 protocols using genespring 12.6.1 platform

Microarray Analysis of Differentially Expressed Genes

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Agilent GeneSpring GX software was used for statistical analysis of the data after microarrays scanning. Differentially expressed genes were determined using one-way ANOVA (analysis of variance) test with asymptotic p values. The criteria used for differentially expressed genes required the absolute value of Fold Change (FC) to be greater than 1 (|FC| > 1) in at least one compared paired samples. The standard cut-off of p value < 0.05 was set to determine statistical significance of mRNA fluorescent signals.
The microarray data analysis was performed with the use of the GeneSpring 12.6.1 platform (Agilent Technologies, Inc., Santa Clara, CA, USA) and PL-Grid Infrastructure. In order to determine which of the differentiating miRNAs of the fibroblast cells exposed to the drug, compared to the control sample, could potentially affect the transcriptional activity of the differentiating mRNAs, the miRNA target prediction tools mirTAR (http://mirtar.mbc.nctu.edu.tw/human/predictionIndex.php) and microRNA.org (http://www.microrna.org/microrna/getGeneForm.do) have been used.

Wcisło-Dziadecka D., Grabarek B., Zmarzły N., Skubis A., Sikora B., Kruszniewska-Rajs C., Gola J., Mazurek U, & Kucharz E. (2018). Influence of Adalimumab on the Expression Profile of Genes Associated with the Histaminergic System in the Skin Fibroblasts In Vitro. BioMed Research International, 2018, 1582173.

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miRNA Expression Profile Analysis

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The analysis of the expression profile of miRNA which are responsible for regulation of histamine-related genes was performed using commercially available GeneChip^® miRNA 2.0 Array (Affymetrix, Santa Clara, CA).
The first step comprised labelling of miRNA with biotin by polyadenylation and ligation. The evaluation of labelling efficiency was verified using ELOS QC Assay (FlashTagBiotin HSR RNA Labeling Kit, Affymetrix). Subsequently the hybridization of labelled RNA molecules of the microarray and probes were scanned using GeneArray Scanner 3000 7G (Agilent Technologies, CA). The scanned data were processed for signal values using Microarray Suite 5.0 software (Affymetrix).
Agilent GeneSpring GX software was used for statistical analysis of the data after microarrays scanning. Differentially expressed genes were determined using one-way ANOVA (analysis of variance) test with asymptotic computation of p-values. The criteria used for differentially expressed genes required the absolute value of fold change (FC) to be greater than 1 (|FC| > 2) in at least one compared sample pairs. The standard cut-off of p-value < 0.05 was set to determine statistical significance of mRNA fluorescent signals. Microarray data analysis was performed with the use of the GeneSpring 12.6.1 platform (Agilent Technologies, Inc., Santa Clara, CA, USA) and PL-Grid Infrastructure.

Wcisło-Dziadecka D., Gola J., Grabarek B., Mazurek U., Brzezińska-Wcisło L, & Kucharz E.J. (2018). Effect of adalimumab on the expression of genes encoding TNF-α signal paths in skin fibroblasts in vitro. Advances in Dermatology and Allergology/Postȩpy Dermatologii i Alergologii, 35(4), 413-422.

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