Geneglobe data analysis software

Manufactured by Qiagen

GeneGlobe data analysis software is a bioinformatics tool developed by Qiagen for the analysis and interpretation of gene expression data. The software provides a platform for researchers to perform various data analysis tasks, including data normalization, differential expression analysis, and pathway enrichment analysis.

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Lab products found in correlation

Rt2 profiler pcr array, by Qiagen (2 mentions) Rt2 first strand kit, by Qiagen (1 mentions) Sybr green qpcr mastermix, by Qiagen (1 mentions) Rt2 sybr green qpcr mastermix, by Qiagen (1 mentions) Version, by MedCalc (1 mentions) Miscript pcr system, by Qiagen (1 mentions) Nanodrop 8000 spectrophotometer, by Thermo Fisher Scientific (1 mentions) Viia 7 real time pcr system, by Thermo Fisher Scientific (1 mentions) Miscript mirna pcr array for mouse fibrosis, by Qiagen (1 mentions) Veriti 96 well thermal cycler, by Thermo Fisher Scientific (1 mentions) Miscript sybr green pcr kit, by Qiagen (1 mentions) Mirneasy mini kit, by Qiagen (1 mentions) Miscript 2 rt kit, by Qiagen (1 mentions) Rneasy mini kit, by Qiagen (1 mentions)

5 protocols using geneglobe data analysis software

Comprehensive Gene Expression Analysis

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To prepare cDNA, extracted RNA was treated with DNAse and reverse-transcribed using the RT2 First Strand Kit (Qiagen 330401) according to manufacturer’s instructions. High quality RNase- free water was then used to dilute the resultant cDNA to a volume of 111 μl. Finally, 102 μl of the cDNA sample was combined with RT2 SYBR Green qPCR Master mix (Qiagen 330503). The mixture of diluted cDNA + SYBR Green qPCR Master mix (Qiagen 330503) was used to determine the expression of 84 Hypoxia genes (Catalog number 330231 PAMM032Z) and 84 Oxidative Stress (Catalog number 330231 PAMM-065ZA) genes in the uterine and placental tissue of the dams collected postpartum. Additionally, 84 Wnt Signaling genes (Catalog number 330231 PAMM-043ZA) and 84 Epigenetic Chromatin Modification genes (Catalog number 330231 PAMM-085ZR) were analyzed in the lungs of offspring collected at PND0, as well as 84 Asthma and Allergy related genes (Catalog number 330231 PAMM-067Z) in lung samples at 11 weeks, using RT2 profiler PCR arrays (Qiagen, USA) according to the manufacturer’s instructions. The resulting threshold cycle (Ct) values were obtained and used to calculate both gene expression and fold change, using the ΔΔCt method with the Qiagen GeneGlobe data analysis software. Housekeeping genes Actb, B2m, Gapdh, and Gusb, were used for normalization.

Cahill K., Johnson T., Perveen Z., Schexnayder M., Xiao R., Heffernan L., Langohr I., Paulsen D., Penn A, & Noël A. (2022). In utero exposures to mint-flavored JUUL aerosol impair lung development and aggravate house dust mite-induced asthma in adult offspring mice. Toxicology, 477, 153272.

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Cd-RWPE1 Erk/MAPK Pathway Analysis

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Gene Globe data analysis software (Qiagen) was used to analyze the Erk/MAPK pathway gene expression profile in Cd-RWPE1 compared to RWPE1 samples. Three biological replicates for each group were pooled together to perform the qPCR RT² array analysis. The C_T cut-off was set to 35. Fold regulation cut off was set to 2. Fold-Change (2^ (- Delta Delta CT)) is the normalized gene expression (2^(- Delta CT)) in the Cd-RWPE1 sample divided by the normalized gene expression (2^ (- Delta CT)) in the parental RWPE1 sample that served as the control. The scatter plot was used to compare the normalized expression of every gene on the array between the Cd-RWPE1 and RWPE1 samples and the visualization was represented by a heat map. Statistical analyses were performed with GraphPad Prism 5 and/or MedCalc version 10.3.2. All quantified data represents an average of at least triplicate samples or as indicated. Error bars represent standard deviation or standard error of the mean as indicated in figure legends. All tests were performed two tailed and p-values <0.05 were considered statistically significant.

Dasgupta P., Kulkarni P., Bhat N.S., Majid S., Shiina M., Shahryari V., Yamamura S., Tanaka Y., Gupta R.K., Dahiya R, & Hashimoto Y. (2020). Activation of the Erk/MAPK signaling pathway is a driver for cadmium induced prostate cancer.. Toxicology and applied pharmacology, 401, 115102.

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Measuring Liver Fibrosis miRNA Profiles

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The expression of miRNA molecules involved in fibrosis was evaluated using a miScript PCR system (Qiagen). Total RNA was isolated from liver samples using the miRNeasy mini kit (Qiagen), which ensured the effective purification of miRNA and total RNA. The concentration and purity of RNA were determined using a NanoDrop 8000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA was reverse-transcribed to cDNA by the miScript II RT kit (Qiagen) using a Veriti 96-Well thermal cycler (Applied Biosystems, Foster City, CA, USA). The miRNA PCR array analysis was performed by the miScript SYBR green PCR kit (Qiagen) and the miScript miRNA PCR array for mouse fibrosis (Qiagen) using a ViiA 7 real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). The PCR array contained primers for the detection of 84 miRNA molecules involved in fibrosis and 12 internal controls. The obtained data were analyzed using the GeneGlobe data analysis software provided by Qiagen.

Ciceu A., Balta C., Herman H., Gharbia S., Ignat S.R., Dinescu S., Váradi J., Fenyvesi F., Gyöngyösi S., Hermenean A, & Costache M. (2021). Complexation with Random Methyl-β-Cyclodextrin and (2-Hidroxypropyl)-β-Cyclodextrin Enhances In Vivo Anti-Fibrotic and Anti-Inflammatory Effects of Chrysin via the Inhibition of NF-κB and TGF-β1/Smad Signaling Pathways and Modulation of Hepatic Pro/Anti-Fibrotic miRNA. International Journal of Molecular Sciences, 22(4), 1869.

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Cd-induced PI3K/Akt Pathway Profiling

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RT² PCR profiler array PAHS-058Z (Qiagen) was used for determining expression of PI3K/Akt pathway members. Samples from three biological replicates from the parental normal cells (PWR1E and RWPE1) and Cd exposed cells (Cd-PWR1E and Cd-RWPE1) were used for RNA extraction. Pooled RNA was used for cDNA synthesis and RT² array analysis. Relative quantification changes in expression of genes between parental and Cd-exposed groups were determined by real time PCR and data analyzed by using Gene Globe Data Analysis Software (Qiagen). The RT2 profiler array has 84 PI3K/Akt pathway genes, five endogenous control genes, positive and negative PCR controls.

Kulkarni P., Dasgupta P., Bhat N.S., Hashimoto Y., Saini S., Shahryari V., Yamamura S., Shiina M., Tanaka Y., Dahiya R, & Majid S. (2020). Role of the PI3K/Akt pathway in cadmium induced malignant transformation of normal prostate epithelial cells.. Toxicology and applied pharmacology, 409, 115308.

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Interferon Receptor Expression Profiling

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We applied the interferons and receptors RT² profiler PCR array (catalog number PAHS-064Z; Qiagen) protocol as provided by the manufacturer. Briefly, we stimulated 3 × 10⁶ PBMCs with IFN-α1, -α2, -α6, or -α14 at 1,000 pg/ml for 6 h. The cells were then harvested and lysed with the RLT lysis buffer. We then extracted RNA using the RNeasy minikit (catalog number 74106; Qiagen) and performed a DNase digest on the columns. Subsequently, we reverse transcribed 1 µg RNA for subsequent PCR on Bio-Rad iQ5. The gene expression analyses were done with Qiagen’s GeneGlobe data analysis software. Gene expression data for each IFN-α-treated sample are reported as fold changes relative to the results for matched untreated controls. Therefore, a value of zero signifies no increase in expression compared with the expression in the control samples. Since most of the genes in this PCR array are upregulated from slightly to very vigorously and only a few were modestly downregulated, we have chosen distinct scales for the up- versus downregulated genes. If we had applied the same scale for up- and downregulated genes, the downregulated ones would not be discernible.

Schlaepfer E., Fahrny A., Gruenbach M., Kuster S.P., Simon V., Schreiber G, & Speck R.F. (2019). Dose-Dependent Differences in HIV Inhibition by Different Interferon Alpha Subtypes While Having Overall Similar Biologic Effects. mSphere, 4(1), e00637-18.

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