Genespring v11

Manufactured by Agilent Technologies

Sourced in United States, United Kingdom

GeneSpring V11.5 is a data analysis software package for life science research. It provides tools for the analysis and visualization of gene expression data from various sources, including microarray and next-generation sequencing experiments.

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Lab products found in correlation

13 protocols using genespring v11

Microarray Data Analysis Protocol

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Microarray results were analyzed using a GenePix 4000 B single-channel scanner (Axon Instruments, Inc., Union City, CA, USA). NimbleScan v.2.5 (Roche NimbleGen, Inc.) was used to read the values of the raw microarray signals (532 nm); these signal values were then corrected and normalized according to the NimbleGen's instructions. GeneSpring v11.0 software (Agilent Technologies, Inc., Santa Clara, CA, USA) was used for statistical analysis, clustering and pathway analysis and visualizations. A threshold value of 2 was established; thus, increases and decreases ≥2-fold were regarded as cases of upregulation and downregulation, respectively.

Cui F.M., Sun X.J., Huang C.C., Chen Q., He Y.M., Zhang S.M., Guan H., Song M., Zhou P.K, & Hou J. (2017). Inhibition of c-Myc expression accounts for an increase in the number of multinucleated cells in human cervical epithelial cells. Oncology Letters, 14(3), 2878-2886.

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Profiling Nerve Tissue Transcriptome

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Total RNA was extracted from sciatic nerve tissue from each group using TRIzol (Invitrogen, Carlsbad, CA, USA) and purified with RNeasy spin columns (Qiagen, Hilden, Germany). The NanoDrop ND-2000 and Agilent Bioanalyzer 2100 instruments (Agilent Technologies, Santa Clara, CA, USA) were used to verify the purified RNA. Microarray was used to detect the changes of mRNA and lncRNA in the distal nerve at 0, 3, 7, and 14 days after PNI through the Array platform (Agilent Technologies). Results were normalized using GeneSpring v11.0 software (Agilent Technologies). The experiments were performed following the manufacturer’s protocols (Yu et al., 2013).

Pan B., Guo D., Jing L., Li K., Li X., Li G., Gao X., Li Z.W., Zhao W., Feng H, & Cao M.H. (2022). Long noncoding RNA Pvt1 promotes the proliferation and migration of Schwann cells by sponging microRNA-214 and targeting c-Jun following peripheral nerve injury. Neural Regeneration Research, 18(5), 1147-1153.

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Microarray Analysis of Mouse Transcriptome

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Microarray analysis was performed using a Mus musculus 12×135k v2 array, which consists of 135 000 amino acid-modified 60-mer oligonucleotide probes representing 44 170 genes (Kangchen Bio Shanghai, China). After preparing 1 μg of DNase-treated total RNA, fluorescent dye (Cy3-dCTP)-labelled cDNA produced via RNA amplification and subsequent enzymatic reaction were then hybridized into an array using the NimbleGen Hybridisation System 4 (Roche NimbleGen, Madison, WI, USA). Finally, the arrays were scanned using a GenePix 4000B single-channel scanner (Molecular Devices, Sunnyvale, CA, USA), and the data were extracted from the obtained images using GenePix Pro v6.0 (Molecular Devices, Sunnyvale, CA, USA). GeneSpring v11.0 software (Agilent Technologies, Santa Clara, CA, USA) was used to analyse the genes that were differentially expressed between the experimental and control groups. The genes that were consistently altered in both arrays with differences in mean expression ratios that were greater than twofold on average were selected as differentially expressed genes. The microarray results were analysed via both gene ontology (GO) and pathway analysis using NimbleScan v2.5 Software (Roche NimbleGen, Madison, WI, USA). Each condition was performed in triplicate.

Shang Z.Z., Li X., Sun H.Q., Xiao G.N., Wang C.W, & Gong Q. (2014). Differentially expressed genes and signalling pathways are involved in mouse osteoblast-like MC3T3-E1 cells exposed to 17-β estradiol. International Journal of Oral Science, 6(3), 142-149.

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Serological Analysis of Biomedical Samples

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Seroreactivity was evaluated by comparing median ODs and MFIs using unpaired Mann-Whitney test between two groups; p-values of the U statistic were computed asymptotically (100 permutations) and Benjamini-Hochberg (B–H) corrected for multiple comparisons. For receiver operator characteristic (ROC) comparisons, the area under the curve (AUC) was computed using the trapezoidal rule, asymptotic normal p-values were Bonferroni corrected for multiple comparisons. ODs comparisons were performed using GeneSpring v11.5 (Agilent Technologies, Santa Clara, CA). All other statistical analyses were performed using Prism v6 (GraphPad, La Jolla, CA) or STATA v11.2 (Statacorp, College Station, TX).

Labo N., Miley W., Marshall V., Gillette W., Esposito D., Bess M., Turano A., Uldrick T., Polizzotto M.N., Wyvill K.M., Bagni R., Yarchoan R, & Whitby D. (2014). Heterogeneity and Breadth of Host Antibody Response to KSHV Infection Demonstrated by Systematic Analysis of the KSHV Proteome. PLoS Pathogens, 10(3), e1004046.

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Differential Expression Analysis of lncRNA and mRNA

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The lncRNA and mRNA array data were analyzed for data summarization, normalization, and quality control using GeneSpring V11.5 software (Agilent). To select differentially expressed genes, we used threshold values of ≥2-fold change, and a Benjamini–Hochberg-corrected p value of 0.05 performed on technically duplicated dots for each lncRNA. The data were Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software. Further analysis was performed by hierarchical clustering with average linkages. Finally, we performed tree visualization using Java TreeView (Stanford University School of Medicine, Stanford, CA, USA).

Qu X., Dang X., Wang W., Li Y., Xu D., Shang D, & Chang Y. (2018). Long Noncoding RNAs and mRNA Regulation in Peripheral Blood Mononuclear Cells of Patients with Chronic Obstructive Pulmonary Disease. Mediators of Inflammation, 2018, 7501851.

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Transcriptome Analysis of Cells Using Microarray

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RNA was isolated from the cells using RiboPure™ kit (Life Technologies, Frederick, MD) and RNA quality was controlled using the Agilent 2100 Bioanalyzer. Gene expression studies were performed using Affymetrix U133 Plus 2.0 (Affymetrix, Santa Clara, CA) human oligonucleotide microarrays containing over 47,000 transcripts and variants, including 38,500 well characterized human genes. After hybridization, the chips were scanned using GeneChip Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Background correction and normalization was done using Iterative Plier 16 with GeneSpring V11.5 software (Agilent, Palo Alto, CA). The criteria for differentially expressed genes was set at ≥2-fold changes (p-value <0.05). The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (Ingenuity Systems, Redwood City, CA) to perform biological network and functional analyses.

ARISI M.F., STARKER R.A., ADDYA S., HUANG Y, & FERNANDEZ S.V. (2014). All trans-retinoic acid (ATRA) induces re-differentiation of early transformed breast epithelial cells. International Journal of Oncology, 44(6), 1831-1842.

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Differential Gene Expression Analysis

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The miRNA and mRNA array data were analyzed for data summarization, normalization and quality control using GeneSpring V11.5 software (Agilent). To select differentially expressed genes, we used threshold values of >2 fold change. The data were Log2 transformed and median centred by genes using the Adjust Data function of CLUSTER 3.0 software. Further analysis was performed by hierarchical clustering with average linkages. Finally, we performed tree visualization using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

Dang X., Qu X., Wang W., Liao C., Li Y., Zhang X., Xu D., Baglole C.J., Shang D, & Chang Y. (2017). Bioinformatic analysis of microRNA and mRNA Regulation in peripheral blood mononuclear cells of patients with chronic obstructive pulmonary disease. Respiratory Research, 18, 4.

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Dysbindin Knockout Mouse Hippocampal Transcriptome

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Four homozygous dysbindin −/− (Sandy) mice and four wild type mice were deeply anaesthetized and killed by decapitation. The brains were harvested and the right hippocampus dissected out and stored in RNA Later (Ambion, Austin, TX, USA). Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. Extracted RNA was purified using the RNeasy® Kit (Qiagen, Hilden, Germany). RNA was extracted from the hippocampus and submitted to the BFIG Core Facility Lab (Department of Paediatrics, National University of Singapore). The quality of RNA was analyzed using an Agilent 2100 Bio-analyzer (Agilent, Santa Clara, CA). cRNA was generated and labeled using the one-cycle target labeling method and hybridized to Affymetrix Mouse Genome 430 2.0 microarrays (Affymetrix, Santa Clara, CA), using standard Affymetrix protocols. A total of eight microarrays were used for the two groups of animals - four for the homozygous dysbindin −/− right hippocampi, and four for the wild type right hippocampi. Initial image analysis of the microarray chips was performed with Affymetrix GCOS 1.2 software. The data were exported into GeneSpring v11 (Agilent) software for analysis using parametric test based on cross gene error model (PCGEM). T-test was used to identify differentially expressed genes between the two groups. P < 0.05 was considered significant.

Chen Y., Bang S., McMullen M.F., Kazi H., Talbot K., Ho M.X., Carlson G., Arnold S.E., Ong W.Y, & Kim S.F. (2016). Neuronal Activity Induced Sterol Regulatory Element Binding Protein-1 (SREBP1) is disrupted in Dysbindin Null Mice – Potential Link to Cognitive Impairment in Schizophrenia. Molecular neurobiology, 54(3), 1699-1709.

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Comparative Analysis of CKD Transcriptome

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Raw CKD patient data from the microarray dataset GSE66494 were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/; accessed on 1 August 2017). These data were normalized with GeneSpring v11 software (Agilent Technologies, Santa Clara, CA, USA) as log₂ values. The boxplot, which was produced using SPSS 22 software (IBM, Armonk, NY, USA), showed the transcriptional activity between CKD patients and healthy individuals.

Hsu Y.H., Zheng C.M., Chou C.L., Chen Y.J., Lee Y.H., Lin Y.F, & Chiu H.W. (2021). Therapeutic Effect of Endothelin-Converting Enzyme Inhibitor on Chronic Kidney Disease through the Inhibition of Endoplasmic Reticulum Stress and the NLRP3 Inflammasome. Biomedicines, 9(4), 398.

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Zebrafish Transcriptomic Analysis of Mutants

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Two-color microarray experiments were performed by the UHN Microarray Facility using the Zebrafish (v.3) 44 k Gene Expression Microarray Platform (Agilent). cDNA was generated from total RNA isolated from pools of 20 WT or m628 mutant embryos at 54 hpf, with two biological replicates used. Microarray results were analyzed using Genespring v.11.0.1 (Agilent), with data normalized using Agilent’s Spatial Detrending and Lowess normalization. After normalization and averaging, data were filtered such that only probes that were between the 20th and 100th percentile of the distribution of intensities in both samples for either group were kept. Statistical significance for differential expression between sample groups was set at p < 0.05.

Burrows J.T., Pearson B.J, & Scott I.C. (2015). An In Vivo Requirement for the Mediator Subunit Med14 in the Maintenance of Stem Cell Populations. Stem Cell Reports, 4(4), 670-684.

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