Abstract
Microarray-based transcriptomic profiling enables simultaneous measurement of expression of multiple genes from one biological sample. Here we describe a detailed protocol, which serves to examine global gene expression using whole genome oligonucleotide microarrays. We also provide examples of bioinformatics tools, which are helpful in analyses and interpretation of microarray data, and propose further biological assays, to warrant conclusions drawn from transcriptomic signature.
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Oberthuer A, Juraeva D, Li L et al (2010) Comparison of performance of one-color and two-color gene expression analyses in predicting clinical endpoints of neuroblastoma patients. Pharmacogenomics J 10:258–266. https://doi.org/10.1038/tpj.2010.53
Slonim DK, Yanai I (2009) Getting started in gene expression microarray analysis. PLoS Comput Biol 5:e1000543. https://doi.org/10.1371/journal.pcbi.1000543
Mi H, Huang X, Muruganujan A et al (2017) PANTHER version 11: expanded annotation data from gene ontology and Reactome pathways and data analysis tool enhancements. Nucleic Acids Res 45:D183–D189. https://doi.org/10.1093/nar/gkw1138
Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative nalysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57
Huber W, Carey VJ, Gentleman R et al (2015) Orchestrating high-throughput genomic analysis with bioconductor. Nat Methods 12(2):115–121. https://doi.org/10.1038/nmeth.3252
Grabiec K, Gajewska M, Milewska M et al (2014) The influence of high glucose and high insulin on mechanisms controlling cell cycle progression and arrest in mouse C2C12 myoblasts: the comparison with IGF-I effect. J Endocrinol Investig 37:233–245
Dedieu S, Mazcres G, Cottin P et al (2002) Involvement of myogenic regulator factors during fusion in the cell line C2C12. Int J Dev Biol 46:235–241
Chomczynski P, Sacchi N (2006) The single step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on. Nat Protoc 1:581–585
Wieteska-Skrzeczyńska W, Grzelkowska-Kowalczyk K, Tokarska J et al (2011) Growth factor and cytokine interactions in myogenesis. Part I. The effect of TNF-α and IFN-γ on IGF-I-dependent differentiation in mouse C2C12 myogenic cells. Pol J Vet Sci 14:417–424
T042-TECHNICAL BULLETIN NanoDrop Spectrophotometers. http://www.nhm.ac.uk/content/dam/nhmwww/our-science/dpts-facilities-staff/Coreresearchlabs/nanodrop.pdf
QIAGEN Newsletter March 15, 2010
Cicinnati VR, Shen Q, Sotiropoulos GC et al (2008) Validation of putative reference genes for gene expression studies in human hepatocellular carcinoma using real-time quantitative RT-PCR. BMC Cancer 8:350. https://doi.org/10.1186/1471-2407-8-350
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B (Methodological) 57:289–300
Stafford P (2008) Methods in microarray normalization. CRC Press Print ISBN: 978-1-4200-5278-7
Morey JS, Ryan JC, Van Dolah FM (2006) Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR. Biol Proced Online 8:175–193
Tarca AL, Romero R, Draghici S (2006) Analysis of microarray experiments of gene expression profiling. Am J Obstet Gynecol 195:373–388
Grabiec K, Majewska A, Wicik Z et al (2016) The effect of palmitate supplementation on gene expression profile in proliferating myoblasts. Cell Biol Toxicol 32:185–198. https://doi.org/10.1007/s10565-016-9324-2
Mi H, Muruganujan A, Casagrande JT et al (2013) Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 8:1551–1566. https://doi.org/10.1038/nprot.2013.092
Grzelkowska-Kowalczyk K, Wicik Z, Majewska A et al (2015) Transcriptional regulation of important cellular processes in skeletal myogenesis through interferon-γ. J Interf Cytokine Res 35:89–99
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Majewska, A., Domoradzki, T., Grzelkowska-Kowalczyk, K. (2019). Transcriptomic Profiling During Myogenesis. In: Rønning, S. (eds) Myogenesis. Methods in Molecular Biology, vol 1889. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8897-6_9
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DOI: https://doi.org/10.1007/978-1-4939-8897-6_9
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