Genespring ver 12

Manufactured by Agilent Technologies

GeneSpring Ver.12.6 is a software solution for the analysis and visualization of genomic data. It provides tools for data processing, statistical analysis, and pathway interpretation. The software is designed to handle large-scale data from various high-throughput technologies, such as microarrays and next-generation sequencing.

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Lab products found in correlation

Genechip human gene 1.0 st, by Thermo Fisher Scientific (1 mentions) Expression console, by Thermo Fisher Scientific (1 mentions) Ht mg 430 pm array, by Thermo Fisher Scientific (1 mentions) High capacity cdna reverse transcription kit, by Thermo Fisher Scientific (1 mentions) Tri reagent, by Merck Group (1 mentions) Agilent microarray scanner g2565ba, by Agilent Technologies (1 mentions) Sureprint g3 human gene expression 8 60 k v2 microarray, by Agilent Technologies (1 mentions) Low input quick amp labeling kit, by Agilent Technologies (1 mentions)

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GeneSpring (227 citations) GeneSpring 12.0 (79 citations)

5 protocols using genespring ver 12

RNA Microarray Analysis of Cell Types

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For human cells, RNA was obtained from WAs, iBAs, and dBAs, and after reverse-transcription, microarray analyses were performed using GeneChip human Gene 1.0 ST (Affymetrix) according to the manufacturer’s instruction. For mouse cells, RNA obtained from MEFs, BAT, and dBAs was reverse-transcribed and analyzed using GeneChip Mouse Genome 430 2.0 Array. Scanned data were analyzed using Expression Console (Affymetrix) and GeneSpring Ver.12.6 (Agilent Technologies) software.

Kishida T., Ejima A., Yamamoto K., Tanaka S., Yamamoto T, & Mazda O. (2015). Reprogrammed Functional Brown Adipocytes Ameliorate Insulin Resistance and Dyslipidemia in Diet-Induced Obesity and Type 2 Diabetes. Stem Cell Reports, 5(4), 569-581.

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Gene Expression Profiling of CIC-DUX4 Sarcoma

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GeneChip analysis was conducted to determine gene expression profiles. The murine HT MG-430 PM array (Affymetrix) was hybridized with aRNA probes generated from eMC 48 h after transduction with pMYs-CIC-DUX4 or empty vector, CDS and ES tumor tissues, or a mixture of mouse normal tissues according to methods described previously (11 (link)). The expression data were analyzed using GeneSpring ver 12.6 (Agilent Technologies) and gene set enrichment analysis (GSEA) was performed using GSEA-P 2.0 software (12 (link)). The microarray data sets are accessible through the NCBI Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo), with an accession number GSE90978.

Yoshimoto T., Tanaka M., Homme M., Yamazaki Y., Takazawa Y., Antonescu C.R, & Nakamura T. (2017). CIC-DUX4 induces small round cell sarcomas distinct from Ewing sarcoma. Cancer research, 77(11), 2927-2937.

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Quantifying Gene Expression in Murine Liver

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Total RNA was isolated from liver using TriReagent^®(Sigma, St. Louis, MO). Reverse transcription was performed using the High
Capacity cDNA Reverse Transcription kit (Applied Biosystems, Carlsbad, CA).
Real-time PCR was performed using an Applied Biosystems 7900 HT instrument with
Taqman Gene Expression assays containing gene specific primers and probes.
Relative gene expression was determined using the comparative cycle threshold
method. Data were normalized to GAPDH and expressed as a
fold-change from C57BL/6J mice fed the control diet for statistical analysis.
Gene expression data were transformed (log2) and plotted in a heatmap generated
with Genespring ver12.6 (Agilent Technologies, Inc., Santa Clara, CA) to aid
visualization of results (Figure 3).

Betancourt A.M., King A.L., Fetterman J.L., Millender-Swain T., Finley R.D., Oliva C.R., Crowe D.R., Ballinger S.W, & Bailey S.M. (2014). Mitochondrial-nuclear genome interactions in nonalcoholic fatty liver disease in mice. The Biochemical journal, 461(2), 223-232.

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Profiling colorectal cancer miRNAs

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The genome-wide miRNA expression levels of the 30 colorectal cancers from the screening set were analyzed by the SurePrint G3 Human miRNA Rel. 16.0 microarray (Agilent Technologies, Santa Clara, CA, USA), which covers 1222 human miRNAs, according to the manufacturer’s protocol. The microarray data were extracted using the GeneSpring ver. 12.5 (Agilent Technologies). The raw data was normalized by using the 90-percentile shift method, and the acquired data of each miRNA were compared between wild-type KRAS/BRAF tumors and mutant-BRAF tumors using Mann-Whitney U test. The microarray data has been deposited in the Gene Expression Omnibus database (accession No. GSE66548).

Takahashi H., Takahashi M., Ohnuma S., Unno M., Yoshino Y., Ouchi K., Takahashi S., Yamada Y., Shimodaira H, & Ishioka C. (2017). microRNA-193a-3p is specifically down-regulated and acts as a tumor suppressor in BRAF-mutated colorectal cancer. BMC Cancer, 17, 723.

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Genome-wide Gene Expression Profiling of Mesenchymal Stem Cells and Osteoblasts

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Genome-wide gene expression was analyzed by a SurePrint G3 Human Gene Expression 8 × 60 K v2 Microarray (Agilent Technologies, Santa Clara, CA). cRNA labeled with Cy3 was synthesized from 200 ng of total RNA using a Low Input Quick Amp Labeling Kit (Agilent Technologies), and 600 ng of Cy3-labeled cRNA was fragmented and hybridized to a SurePrint G3 Gene Expression Microarray at 65 °C for 17 hours. Then, the microarray was scanned using an Agilent G2565BA microarray scanner (Agilent Technologies). The obtained signals were processed by Feature Extraction Ver.9.1 (Agilent Technologies), and analyzed by GeneSpring Ver.12.5 (Agilent Technologies). The signal intensity of each probe was normalized so that the 75th percentile of signal intensity of all the probes would be 1.0, and the mean signal intensity of all the probes within a specific gene was used as an expression level of the gene. Gene expression data of mesenchymal stem cells (n = 7, GSE28974) and osteoblasts (n = 3, GSE33382) were obtained from GEO.

Asano N., Takeshima H., Yamashita S., Takamatsu H., Hattori N., Kubo T., Yoshida A., Kobayashi E., Nakayama R., Matsumoto M., Nakamura M., Ichikawa H., Kawai A., Kondo T, & Ushijima T. (2019). Epigenetic reprogramming underlies efficacy of DNA demethylation therapy in osteosarcomas. Scientific Reports, 9, 20360.

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