Developmental time points (DAF) were chosen for pooling based on maximal transcript levels of two key enzymes of galactomannan biosynthesis, galactosyl transferase and mannan synthase [ 4, 14, 20].
PASA acts to subsume equivalent alignments to form a number of maximal transcript assemblies (termed maximum transcripts) that represent alternative mRNA isoforms consistent with the data from the alignment cluster.
General transcriptome statistics, including maximal transcript length, mean transcript length and N50, of the resulting transcriptome were calculated with a custom R script.
All show maximal transcript levels in seedling roots.
One (Accession no. CD747033) reached maximal transcript abundance at 48 hours PBM, the expected expression pattern.
In contrast to in vivo data [ 30, 47], in ES cells grown and RA-treated in culture, we found no clear correlation between the timing of maximal expression (transcript level) of individual Hoxb genes and their position in the cluster.
Furthermore, maximal differential transcript levels of any p value were of ~36-fold in fins, while only of ~10 fold in organs.
The transcript matrix U is defined as a binary matrix, where and k is a parameter determining the maximal number of transcripts returned by the algorithm.
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.
Pre-assemblies were finally reconciled using CAP3 with default parameters to provide the maximal set of transcripts for each transcriptome.
