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To determine the specificity of the observed metabolite changes to HTLV1 transformation, we performed LAESI experiments on non-HTLV3 transformed 293T kidney epithelial cells, and on HTLV3 and Tax3 transfected 293T cells.
To confirm the rice transformation, we performed PCR analysis using primers designed to amplify the Z3 transgene and confirmed all six independent T1 transgenic plants (Additional file 4: figure S4a).
To determine if the p38 MAPK pathway is required for endurance exercise-induced fiber-type transformation, we performed fiber-type analysis.
To investigate a possible direct role for Mitostatin in prostate cells transformation we performed anchorage-independent growth assays and an in vivo tumorigenicity in nude mice.
To further investigate whether Rab2A is sufficient to induce transformation, we performed soft-agar colony formation assay on Rab2A-overexpressing and control vector cells.
To assess the effects of miR-494 inhibition on transformation, we performed soft agar colony-formation assays and scored the number of colonies formed after 2 weeks.
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Because of the non-normal distribution of the data, even after transformations, we performed analysis using a generalized linear model with a single factor (i.e., species) using a Poisson distribution unless otherwise stated.
The three transformations we perform are as follows: Abstraction: identification of GO or ChEBI terms embedded in a longer GO term, and replacement of this embedded term with a generic GTERM token, for an embedded GO term, or CTERM token, for an embedded ChEBI term.
To preclude false identification of genes as essential due to low transformation frequencies, we performed experiments to optimize the transformation efficiency of S. sanguinis SK3626.
To further investigate the transformation mechanism, we performed an experiment in which purified plasmid DNA was added.
After logarithmic transformation of PPT, we performed z transformation as previously described (Wylde et al. 2012) in order to analyze the proportion of altered values.
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