Myogenic Differentiation Transcriptome Analysis

Total RNA was prepared from DsRed+ cells, DsRed+ cells allowed to undergo myogenic differentiation for 5 days, DECT+ cells, and DECT+ cells allowed to undergo myogenic differentiation for 5 days. RNA was isolated using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and purified as previously described (Ozawa and Kobayashi, 2014 (link)). cRNA was amplified and labeled using a Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) and hybridized to a 44K Agilent 60-mer oligomicroarray (Mouse Oligo Microarray Kit). The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Agilent Feature Extraction Software (version 9.5.1.1). Microarray data analysis was supported by Cell Innovator (Fukuoka, Japan).

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, & Ozawa M. (2015). E-cadherin cytoplasmic domain inhibits cell surface localization of endogenous cadherins and fusion of C2C12 myoblasts. Biology Open, 4(11), 1427-1435.

Publication 2015

TRIzol Reagent Quick Amp Labeling Kit Agilent scanner Feature Extraction Software (version 9.5.1.1).

Cell Crna Hybridization Microarray analysis Mouse Myogenic Oligo Trizol

Corresponding Organization : Kagoshima University

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Variable analysis

independent variables

Cell type: DsRed+ cells, DsRed+ cells allowed to undergo myogenic differentiation for 5 days, DECT+ cells, DECT+ cells allowed to undergo myogenic differentiation for 5 days

dependent variables

Relative hybridization intensities and background hybridization values measured using Agilent Feature Extraction Software

control variables

RNA isolation using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and purification as previously described (Ozawa and Kobayashi, 2014)
CRNA amplification and labeling using a Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA)
Hybridization to a 44K Agilent 60-mer oligomicroarray (Mouse Oligo Microarray Kit)
Microarray scanning using an Agilent scanner

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

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