Gene spring software 12

Manufactured by Agilent Technologies

Sourced in United States

Gene Spring Software 12.6 is a bioinformatics software platform designed for the analysis and visualization of genomic data. It provides a comprehensive suite of tools for gene expression analysis, pathway analysis, and data integration.

Automatically generated - may contain errors

Lab products found in correlation

37 protocols using gene spring software 12

miRNA Array Analysis of Drosha Knockdown

Check if the same lab product or an alternative is used in the 5 most similar protocols

The miRNA array assay was performed as described previously in detail.^{27 (link)} The MGC-803/Drosha-shRNA and MGC-803/NC-shRNA control cells were used in the Agilent miRNA array (Agilent, Santa Clara, CA, USA). The raw data were normalized by Quantile algorithm using the Gene Spring Software12.6 (Agilent, Santa Clara, CA, USA). These miRNAs were then grouped using hierarchical clustering with ‘complete' using Heatmap.2 function (gplots package v.2.9.0).
The potential target genes for the dysregulation miRNAs were predicted using TargetScan v.6.2 algorithms, miRanda algorithms and DIANA-microT algorithms software (WWW.microrna.gr/WebServer) as described previously.^{27 (link)} All the copredicted target genes were used for subsequent functional analysis through DAVID Bioinformatics Resources 6.7. The P-value cutoff was set below 0.05.

Xu L., Hou Y., Tu G., Chen Y., Du Y.E., Zhang H., Wen S., Tang X., Yin J., Lang L., Sun K., Yang G., Tang X, & Liu M. (2017). Nuclear Drosha enhances cell invasion via an EGFR-ERK1/2-MMP7 signaling pathway induced by dysregulated miRNA-622/197 and their targets LAMC2 and CD82 in gastric cancer. Cell Death & Disease, 8(3), e2642-.

+ Open protocol

+ Expand

miRNA Profiling of Irradiated MLE-12 Cells with mMSCs-Exos

Check if the same lab product or an alternative is used in the 5 most similar protocols

The miRNA profile between irradiated MLE-12 cells with or without mMSCs-Exos treatment was performed at KangCheng Biotechnology Corporation (Shanghai, China). Agilent Mouse miRNA microarray (Agilent Technologies, USA) was used in the analysis. According to the manufacturer’s protocol, miRNAs were labeled and hybridized with miRNA complete Labeling and Hybridization kit. Data normalization and processing were performed using Quantile algorithm, Gene Spring Software 12.6 (Agilent Technologies, USA). The differential expression of miRNAs was performed via the Pearson’s correlation analysis with Cluster 3.0 and TreeView software, and the differentially expressed genes (DEGs) were identified to have at least |logFC| > 2, p value < 5% in expression.

Li Y., Shen Z., Jiang X., Wang Y., Yang Z., Mao Y., Wu Z., Li G, & Chen H. (2022). Mouse mesenchymal stem cell-derived exosomal miR-466f-3p reverses EMT process through inhibiting AKT/GSK3β pathway via c-MET in radiation-induced lung injury. Journal of Experimental & Clinical Cancer Research : CR, 41, 128.

+ Open protocol

+ Expand

Agilent Human lncRNA and mRNA Microarrays

Check if the same lab product or an alternative is used in the 5 most similar protocols

The Agilent Human 4 × 180 K lncRNA and mRNA Microarrays (Agilent, Santa Clara, CA, USA) were performed using a Gene Expression Hybridization Kit (Agilent, Santa Clara, CA, US) according to the manufacturer’s instructions. Slides were washed in staining dishes with a Gene Expression Wash Buffer Kit (Agilent, Santa Clara, CA, USA) and scanned by an Agilent Microarray Scanner (Agilent, Santa Clara, CA, USA) with default settings according to the manufacturer’s instructions. Raw data were normalized by Quantile algorithm using Gene Spring Software 12.6 (Agilent Technologies). The differentially expressed lncRNAs and mRNAs were identified by using R software (version 3.2.3) with the samr package53 (link).

Wang W., Gao F., Zhao Z., Wang H., Zhang L., Zhang D., Zhang Y., Lan Q., Wang J, & Zhao J. (2017). Integrated Analysis of LncRNA-mRNA Co-Expression Profiles in Patients with Moyamoya Disease. Scientific Reports, 7, 42421.

+ Open protocol

+ Expand

Differential miRNA Expression in Lung Cancer

Check if the same lab product or an alternative is used in the 5 most similar protocols

The discovery cohort included plasma samples from 3 patients with ALK-positive lung cancer, 3 patients with ALK-negative lung cancer, and 3 healthy volunteers. These samples were analyzed by Agilent human microRNA microarray chips (8*60 K), V21.0. The data were extract via Agilent Feature Extraction Software (v10.7). Using the quantile algorithm in GeneSpring Software 12.6 (Agilent), the raw data were normalized. MicroRNAs with differential expression of 2-fold changes or more were sifted.

Li L.L., Qu L.L., Fu H.J., Zheng X.F., Tang C.H., Li X.Y., Chen J., Wang W.X., Yang S.X., Wang L., Zhao G.H., Lv P.P., Zhang M., Lei Y.Y., Qin H.F., Wang H., Gao H.J, & Liu X.Q. (2017). Circulating microRNAs as novel biomarkers of ALK-positive non-small cell lung cancer and predictors of response to crizotinib therapy. Oncotarget, 8(28), 45399-45414.

+ Open protocol

+ Expand

Exosomal miRNA microarray profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols

Exosomal miRNAs microarray analysis was performed at Biomarker Technologies (Beijing, China), using Agilent Human miRNA 8*60 K V21.0 microarray (Agilent Technologies, USA). The NCBI BioProject database accession number is PRJNA600674. Gene Spring Software 12.6 (Agilent Technologies) was used for quantile normalization and data processing. Besides, Pearson’s correlation analysis through Cluster 3.0 and TreeView software was used for Hierarchical clustering analysis of the differential expression of miRNAs.

Gong Y., Kong T., Ren X., Chen J., Lin S., Zhang Y, & Li S. (2020). Exosome-mediated apoptosis pathway during WSSV infection in crustacean mud crab. PLoS Pathogens, 16(5), e1008366.

+ Open protocol

+ Expand

Microarray Data Normalization Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

Slides were scanned by Agilent Microarray Scanner (Cat. number G2565CA, Agilent Technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US) with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 12.6 (Agilent Technologies, Santa Clara, CA, US).

Liu Y., Fu W., Lu M., Huai S., Song Y, & Wei Y. (2016). Role of miRNAs in Epicardial Adipose Tissue in CAD Patients with T2DM. BioMed Research International, 2016, 1629236.

+ Open protocol

+ Expand

Comprehensive miRNA Profiling Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

The total RNAs were dephosphorylated by phosphatase and incubated with the Labeling Spike-In kit (Agilent Technologies Inc.) at 37°C for 30 min. The dephosphorylated RNAs were denatured by dimethyl sulfoxide (DMSO) and subsequently incubated at 16°C in a circulating water-bath or cool block for 2 h. The labeled RNAs were purified with spin columns to remove DMSO in the samples, dried in vacuum concentrators at 45–55°C for 1 h and dissolved in nuclease-free water. The dissolved RNAs were mixed with Hyb Spike-In solution (Agilent Technologies Inc.) to assemble the hybridization mixture. The mixture was hybridized to the Agilent Human miRNA array V19.0 (Agilent Technologies Inc.), which covers 2,006 human miRNAs, at 55°C for 20 h. The arrays were washed with the Gene Expression Wash Buffer kit and subsequently scanned by the Agilent Microarray Scanner (both from Agilent Technologies Inc.). Data on miRNA microarray images were extracted by Feature Extraction software 10.7.1.1 and normalized by Gene Spring software 12.6 (both from Agilent Technologies, Inc.). The similarity between the samples was analyzed by the principal component analysis (PCA) and correlation plot.

Wang M., Liang L., Li L., Han K., Li Q., Peng Y., Peng X, & Zeng K. (2017). Increased miR-424-5p expression in peripheral blood mononuclear cells from patients with pemphigus. Molecular Medicine Reports, 15(6), 3479-3484.

+ Open protocol

+ Expand

Profiling miRNA Expression in MGC-803 Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols

The MGC-803/Drosha-shRNA (MGC-803/Drosha KD) and MGC-803/NC-shRNA (MGC-803/Drosha WT) control cells were used in the Agilent miRNA array (Agilent, Santa Clara, CA, USA). The raw data were normalized by Quantile algorithm using the Gene Spring Software12.6 (Agilent, Santa Clara, CA, USA). The different miRNAs were then grouped using hierarchical clustering with ‘complete’ using Heatmap.2 function (gplots package v.2.9.0).

Zhao M., Hou Y., Du Y.E., Yang L., Qin Y., Peng M., Liu S., Wan X., Qiao Y., Zeng H., Cui X., Teng Y, & Liu M. (2020). Drosha-independent miR-6778-5p strengthens gastric cancer stem cell stemness via regulation of cytosolic one-carbon folate metabolism. Cancer letters, 478, 8-21.

+ Open protocol

+ Expand

Microarray-based miRNA Expression Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols

Microarray hybridization experiment was conducted for profiling differentially expressed miRNAs between the two groups. Each slide was hybridized with 100 ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat #5190–0456, Agilent Technologies) in hybridization oven (Cat #G2545A, Agilent Technologies) at 55°C at a rotation speed of 20 rpm for 20 h. After hybridization, slides were washed in staining dishes (Cat #121, Thermo Shandon, USA) with Gene Expression Wash Buffer Kit (Cat #5188–5327, Agilent Technologies). Slides were scanned by Agilent Microarray Scanner (Cat #G2565CA, Agilent Technologies) and analyzed by Feature Extraction software 10.7 (Agilent Technologies) with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 12.6 (Agilent Technologies).

Li Y.H., Yang Y., Yan Y.T., Xu L.W., Ma H.Y., Shao Y.X., Cao C.J., Wu X., Qi M.J., Wu Y.Y., Chen R., Hong Y., Tan X.H, & Yang L. (2018). Analysis of serum microRNA expression in male workers with occupational noise-induced hearing loss. Brazilian Journal of Medical and Biological Research, 51(3), e6426.

+ Open protocol

+ Expand

Exosomal lncRNA Microarray Analysis and Target Prediction

Check if the same lab product or an alternative is used in the 5 most similar protocols

Exosomal lncRNAs microarray analysis was performed at the Shanghai Biotechnology Corporation (Shanghai, China), using Agilent Human miRNA 8*60K V21.0 microarray (Agilent Technologies, USA). Quantile normalization and subsequent data processing were performed using Quantile algorithm, Gene Spring Software 12.6 (Agilent Technologies). The expression of lncRNAs with a FC abs ≥2 was considered significantly changed, and genes in the upstream and downstream of lncRNA within the range of 10 kb were selected as cis-target genes for lncRNAs. According to the prediction of trans-target genes, those genes having complementary or similar sequence with lncRNAs were selected, the complementary energy between the two sequences was then calculated by RNAplex, and genes with e≤−30 were selected as the trans-target genes of lncRNAs. Go and KEGG analysis of predicted target genes were performed through DAVID (https://david.ncifcrf.gov/) (20 (link)).

Song L., Qian G., Huang J., Chen T, & Yang Y. (2021). AZD9291-resistant non-small cell lung cancer cell-derived exosomal lnc-MZT2A-5:1 induces the activation of fibroblasts. Annals of Translational Medicine, 9(20), 1593.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!