For each condition, quantification of transcript expression was performed by using eXpress [ 35] to calculate the fragments per kilobase per million (FPKM) for each transcript.
The average number of newspaper articles each day during the period was 137 (s.d.126), with a maximum of 408 on April 30 and a minimum of 22 on May 25. Television and radio broadcast transcripts were also searched with the same search condition, and the number of transcripts was found to be correlated to the number of newspaper articles during the period of our analysis (r = 0.91).
While the transcripts of RR13 were detected in all organs and conditions following 30 cycles of amplification, 10 additional cycles were needed to detect in all organs and conditions the transcripts of RR12, 14, 16 and 19.
Collectively, the results demonstrate that while some families show differential transcriptional patterns in response to growth conditions, a few stable "core" of transcripts, especially within highly transcribed CAZyme families in strain C1A, appears to be consistently predominant.
Those conditions trigger early maximal upregulation of transcripts [54] and transiently delay seedling growth [46], enabling us to study the link between transcriptional change and subsequent development.
To detect distinct expression differences between the growth conditions, paired Student t-tests of transcripts differentially expressed in ANOVA (FDR < 0,05) have been applied.
As shown in Figure 3, the normalized cDNA obtained from hyphae grown in rich and nutrient-starved conditions encoded a broad set of transcripts represented within the molecular function gene ontologies.
RNA samples were prepared from plants grown under 63 different conditions to increase the variation of transcripts in the libraries (see Additional file 1: Micro-Tom tissues used for RNA preparation).
Cultures were harvested during log phase growth in a variety of conditions to maximize the diversity of transcripts: at intervals at 7 am, 12 pm, 4 pm and 9 pm; after sitting in a dark enclosure for 24 hours; and after being exposed to 20 min of -20°C.
After generating first-strand cDNA from total RNA using ThermoScript RT-PCR System (Life Technologies, Tokyo Japan), PCR was performed with AccuPrime™ Pfx DNA Polymerase (Life Technologies) under the following cycling conditions of either 35 (LTR transcripts) or 25 cycles (others): 95 °C for 1 min; 56 °C (β-actin) or 58 °C (others) for 1 min; and 72 °C for 1 min.
