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Geneglobe

Manufactured by Qiagen
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Sourced in Germany, United States

The GeneGlobe is a laboratory equipment product designed for gene expression analysis. It facilitates the identification and quantification of specific gene transcripts within biological samples. The GeneGlobe provides a platform for researchers to explore gene expression patterns and investigate cellular processes.

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Lab products found in correlation

Rt2 first strand kit, by Qiagen (5 mentions) Qiaseq mirna library kit, by Qiagen (3 mentions) Rneasy mini kit, by Qiagen (2 mentions) Rt2 sybr green qpcr mastermix, by Qiagen (2 mentions) Lna primers, by Qiagen (2 mentions) Mircury lna universal rt mirna pcr system, by Qiagen (2 mentions) Mircury isolation kit, by Qiagen (2 mentions) Iq sybr green supermix kit, by Bio-Rad (2 mentions) Cfx384, by Bio-Rad (2 mentions) Rt2 profiler pcr array, by Qiagen (2 mentions) Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (2 mentions) Nanodrop, by Thermo Fisher Scientific (2 mentions) Sas program, by SAS Institute (2 mentions) Rnalater stabilization solution, by Thermo Fisher Scientific (1 mentions) Viia 7 real time pcr system, by Thermo Fisher Scientific (1 mentions) Spss statistics version 25, by IBM (1 mentions) Nextseq 2000 system, by Illumina (1 mentions) Kapa library quantification kit, by Roche (1 mentions) Truseq stranded mrna sample preparation kit, by Illumina (1 mentions) Quantstudio 6 flex real time pcr, by Thermo Fisher Scientific (1 mentions)

34 protocols using geneglobe

1

Quantifying Lactate and Glucose Impacts

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Lactate and glucose concentrations were compared between groups by analysis of variance (ANOVA) in GraphPad Prism (v. 5.01; GraphPad Software).
Cycle threshold (Ct) values, the number of PCR cycles required for florescent signal to exceed background levels, are inversely proportional to the amount of target nucleic acid present in the sample. Ct values were exported and then uploaded onto GeneGlobe, Qiagen's data analysis web portal (GeneGlobe.qiagen.com">https://GeneGlobe.qiagen.com). Within the GeneGlobe platform, ΔCt values were calculated by subtracting the Ct value for the reference gene (GAPDH) from the Ct value for target genes for each sample. For all experiments, controls were MCF7 cells cultured in glucose/glutamine-free media with 0 mM lactate for 6 h to eliminate the impact of glucose-derived endogenous lactate production (Warburg Effect) on gene expression. Statistical tests were performed on raw ΔCt values for each group. Fold change was then calculated using 2−ΔΔCT formula. Gene expression differences between experimental groups and controls are expressed as fold-regulation. Criteria for reporting gene expression differences include: fold-regulation of ≥2.0 with a p-value of ≤0.05. Lactate and glucose concentrations were compared between groups by analysis of variance (ANOVA) in GraphPad Prism (v. 5.01; GraphPad Software).
San-Millán I., Julian C.G., Matarazzo C., Martinez J, & Brooks G.A. (2020). Is Lactate an Oncometabolite? Evidence Supporting a Role for Lactate in the Regulation of Transcriptional Activity of Cancer-Related Genes in MCF7 Breast Cancer Cells. Frontiers in Oncology, 9, 1536.
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2

CMS Classification of Colorectal Cancer Tumors

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The CMS classification of 31 CRC tumors was obtained using 3′ RNA sequencing, as previously described [21 (link)]. Briefly, tissue homogenization (using Fastprep-24 (MP Biomedicals, Irvine, CA, USA)), RNA extraction (RNeasy Mini Kit (Qiagen, Hilden, Germany)), the evaluation of total tumor RNA amounts (NanodropND-100 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and quality evaluation (2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA)) were performed, before using the QIAseq UPX 3′ transcriptome kit (Qiagen) to generate transcriptomic data. Primary analysis was then performed using GeneGlobe (Qiagen, GeneGlobe">www.qiagen.com/GeneGlobe, accessed on 2 September 2020), and the R package CMS classifier was used to determine the CMS classification of the CRC tumors.
Ducoin K., Bilonda-Mutala L., Deleine C., Oger R., Duchalais E., Jouand N., Bossard C., Jarry A, & Gervois-Segain N. (2022). Defining the Immune Checkpoint Landscape in Human Colorectal Cancer Highlights the Relevance of the TIGIT/CD155 Axis for Optimizing Immunotherapy. Cancers, 14(17), 4261.
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3

Quantifying Cellular Differentiation in Arsenic Exposure

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To initially assess changes over the continuous exposure, RNAs from differentiated control and arsenic-exposed P19 cells at Weeks 8 and 32 were analyzed using a Qiagen RT2 Profiler Cell Lineage PCR Profiler Array (Germantown, MD). This array detects expression of a suite of 84 genes involved in cellular differentiation. RNA was extracted using TRIzol, and RNA concentration and purity were determined on a NanoDrop (Thermo Fisher). A Qiagen RT2 First Strand Kit was used to synthesize complementary DNA (cDNA) from 2 μg of RNA from control and arsenic-exposed treatments (n = 3). Quantitative polymerase chain reaction (PCR) was then conducted with SYBR Green PCR Master Mix (Applied Biosystems, Foster City, CA). Array data were analyzed using Qiagen’s GeneGlobe (GeneGlobe.qiagen.com/us/analyze/">https://GeneGlobe.qiagen.com/us/analyze/), and fold changes were calculated between control and arsenic-exposed cells at each time point.
McMichael B.D., Perego M.C., Darling C.L., Perry R.L., Coleman S.C, & Bain L.J. (2020). Long-term arsenic exposure impairs differentiation in mouse embryonal stem cells. Journal of applied toxicology : JAT, 41(7), 1089-1102.
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4

RNA extraction and qRT-PCR analysis

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Cells were lysed and RNA extracted according to the RNeasy Mini kit (Qiagen, Hilden, Germany). The cDNA synthesis was performed using the SuperScript III First-Strand Synthesis SuperMix (Invitrogen, Waltham, MA, USA). Finally, qRT-PCR was performed using the QuantiTect SYBR Green PCR kit (Qiagen) on a QuantStudio 6 flex qPCR device (Thermo Fisher Scientific, Waltham, MA, USA). Primers for GAPDH (Geneglobe ID: QT00079247) and ADRB2 (Geneglobe ID: QT00200011) were purchased from Qiagen and primers for mEGFP-ADRB2 were self-made (refer to “Oligonucleotides”).
Gmach P., Bathe-Peters M., Telugu N., Miller D.C, & Annibale P. (2022). Fluorescence Spectroscopy of Low-Level Endogenous β-Adrenergic Receptor Expression at the Plasma Membrane of Differentiating Human iPSC-Derived Cardiomyocytes. International Journal of Molecular Sciences, 23(18), 10405.
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5

PCR Array Data Statistical Analysis

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PCR array data were statistically evaluated by Qiagen Gene Globe, as recommended by the manufacturer (Qiagen Gene Globe. Available online: https://geneglobe.qiagen.com/us/, accessed on 6 August 2021). Statistical significance was determined as p < 0.05; the threshold of fold regulation was ±2. Three biological replicates were evaluated in each group. Real-time PCR expression levels were calculated using the ∆∆CT method and the results were analysed using a 2-tailed t-test. Reactions were performed in triplicate for each sample.
Kratochvilova A., Ramesova A., Vesela B., Svandova E., Lesot H., Gruber R, & Matalova E. (2021). Impact of FasL Stimulation on Sclerostin Expression and Osteogenic Profile in IDG-SW3 Osteocytes. Biology, 10(8), 757.
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6

Aorta RNA Extraction and RT-qPCR

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The aortas were immediately after extraction stored in RNAlater Stabilization Solution (ThermoFisher, MA, USA) for 24 h at 5 °C before removed from the solution and stored at − 80 °C until further use. All reagents and kits were purchased from QIAGEN (Hilden, Germany). Total RNA was extracted with TRIzol® Reagent and reverse-transcribed into cDNA using the RT2 First Strand Kit. Two different arrays were used: Rabbit wound healing array (QIAGEN, PANZ-121ZA-RT2 Profiler PCR Array) and a custom array (QIAGEN, CLAN32799A—Custom RT2 PCR Array). Plates were read on the Mx3000P real-time PCR system (Stratagene, CA, USA). The results were analyzed using the online software GeneGlobe (QIAGEN). Gene expression levels of genes-of-interest (GOI) were normalized to the level of the reference genes ACTA2, ACTB, GAPDH, LDHA, and non-POU domain containing octamer-binding-like (LOC100346936). The data was analyzed using the 2-deltaCt method.
Grandjean C.E., Pedersen S.F., Christensen C., Dibenedetto A., Eriksen T., Binderup T, & Kjaer A. (2023). Imaging of atherosclerosis with [64Cu]Cu-DOTA-TATE in a translational head-to-head comparison study with [18F]FDG, and Na[18F]F in rabbits. Scientific Reports, 13, 9249.
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7

Profiling Wnt and Epigenetic Genes

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We used RT2 profiler PCR arrays (Qiagen, USA), according to the manufacturer’s instructions, to assess the expression of 84 Wnt Signaling genes (Catalog number 330231 PAMM-043ZA) and 84 Epigenetic Chromatin Modification genes (Catalog number 330231 PAMM-085ZR) in the lungs of offspring collected at PND5 and PND11. We calculated gene expression and fold changes via the ΔΔCt method with the Qiagen GeneGlobe data analysis software.
Cahill K.M., Gartia M.R., Sahu S., Bergeron S.R., Heffernan L.M., Paulsen D.B., Penn A.L, & Noël A. (2021). In utero exposure to electronic-cigarette aerosols decreases lung fibrillar collagen content, increases Newtonian resistance and induces sex-specific molecular signatures in neonatal mice. Toxicological Research, 38(2), 205-224.
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8

Comparative miRNA Profile in Melanoma

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Primary and metastatic cell cultures were subjected to a comparative evaluation of the expression level of 84 miRNA molecules potentially involved in melanoma invasion and metastasis, in biological triplicate, using miProfile™ human miRNA qPCR arrays (GeneCopoeia) and a Viia7 Real-Time PCR System (Applied Biosystems). Data analysis was performed using the Data Analysis System from the manufacturer (https://www.genecopoeia.com/product/qpcr/analyse/, accessed on 9 October 2022), based on the 2−∆∆Ct method, with normalization of the raw data to several small RNA molecules as an endogenous reference (U6, SNORD44, SNORD47, SNORD48, SNORD49A, SNORD68). Corresponding heatmaps were generated through the use of GeneGlobe (Qiagen), and statistical analysis for the miRNAs of interest was performed using GraphPad Prism software (version 9.0), ANOVA algorithm and Bonferroni correction. Data are expressed as the mean ± SD; p < 0.05 was considered statistically significant. Functional analysis and visual exploration of miRNA-target interactions in a network context was determined using miRNet 2.0. platform [11 (link)].
Lazăr A.D., Dinescu S., Sleiman L., Dumitru A.V., Costache M, & Costache M. (2023). Comparative Expression Profiling Reveals Molecular Markers Involved in the Progression of Cutaneous Melanoma towards Metastasis. International Journal of Molecular Sciences, 24(7), 6565.
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9

Comparative Analysis of NHDF-ASC Co-Cultures

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Normality was assessed with Shapiro–Wilk Tests of Normality. Equality of variances was assessed with Levene’s Test. ELISA data and cell count data from NHDF monocultures were analyzed using repeated measures ANOVA. Quantified immunocytochemistry data and quantified western blot data were analyzed using independent samples t-test. Above tests were performed using IBM SPSS Statistics version 25. Comparison of ELISA data from co-cultures with the sum of data from NHDF monocultures and ASC monocultures was performed using mixed models in SAS version 9.4. RT2 Profiler PCR Array data were analyzed using GeneGlobe (Qiagen, assessed August 2021), in which Cq values of the genes of interest were normalized to the geometric mean of the reference genes. Differences in expression levels were calculated using independent samples t-test of 2−ΔCq values between the experimental groups. Graphs and plots were created using SPSS and GeneGlobe. Data are presented as mean ± standard error. A p-value < 0.05 was considered statistically significant.
Søndergaard R.H., Højgaard L.D., Reese-Petersen A.L., Hoeeg C., Mathiasen A.B., Haack-Sørensen M., Follin B., Genovese F., Kastrup J., Juhl M, & Ekblond A. (2022). Adipose-derived stromal cells increase the formation of collagens through paracrine and juxtacrine mechanisms in a fibroblast co-culture model utilizing macromolecular crowding. Stem Cell Research & Therapy, 13, 250.
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10

Transcriptome and miRNA Sequencing Analysis

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mRNA-seq and miRNA-seq were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA, USA) and QIAseq miRNA Library Kit (Qiagen) according to the manufacturer’s instructions, respectively. Optionally, size selection of library for miRNA sequencing was performed using 6% TBE polyacrylamide gel (Invitrogen). Electrophoresis was performed at 120 V for 1 h in Tris–borate-EDTA (TBE) buffer, and the band of interest (173 bp) was eluted using a Spin-X Centrifuge Tube Filter column (Corning Caster).
Each library was quantified by qPCR using the KAPA Library Quantification kit (KAPA). The quantified libraries were mixed at equimolar ratios, and the diluted library pool was loaded onto a NextSeq 1000/2000 P2 reagent v3 (100 Cycles) cartridge with a mixture of 75 pM and 1% phiX, and run on a NextSeq 2000 system (Illumina) in paired-end × 100 nucleotide multiplex and sequenced according to the manufacturer’s instructions. The resulting FASTQ files were analyzed with BaseSpace DRAGEN RNA Pipeline (Illumina) and Gene Globe (Qiagen).
Yoshida M., Matsuzaki J., Fujita K., Kimura M., Umezu T., Tokuda N., Yamaguchi T., Kuroda M., Ochiya T., Saito Y, & Kimura K. (2024). Plasma extracellular vesicle microRNAs reflecting the therapeutic effect of the CBP/β-catenin inhibitor PRI-724 in patients with liver cirrhosis. Scientific Reports, 14, 6266.
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