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These curves have been obtained by using the expressions reported in Section 3.3.
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For gene expression analysis, we used the expression data reported by Su and colleagues [ 17].
The relative expression was calculated using the expression 2-▽▽CT and reported as arbitrary units [ 31].
RNA from pulverized tumor and adjacent tissue was prepared as described [ 24], reverse transcribed and analyzed by quantitative RT-PCR as reported previously [ 25] using the expression of TATA-box binding protein (TBP) as a reference for normalization.
We used the expressions (3) and (4) reported in the literature [24].
We conclude that IFP represents an excellent reporter for high-throughput protein expression and analysis, which can be easily extended to numerous other expression hosts using the setup reported here.
We used the expression data (read counts) reported in Wang et al. [ 48], and processed it in the same way as our sugarcane data (see above).
TS expression was assessed using the commonest reported method; a semiquantative grading of tumour tissue for chromagen intensity from 0 to 3, with the highest tumour staining detected as the reference for classification.
We therefore used the expression of GFP to report transcription of Siglecg.
Probe sets were initially filtered on the basis of gene expression using the present/marginal/absent calls reported on each chip.
We employed the yeast model [ 50] derived from Lange [ 51] and used the reported gene-expression measurements to constrain the GX-FBA model.
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