The depth of GO annotation varied among transcripts; therefore, for functional definitions described in the results we conducted additional classification of genes based on UniProt annotations and a review of the literature.
Reads were error-corrected using ALLPATHS-LG tool [ 30], and assembled using Trinity software [ 31] to produce transcriptome assemblies that varied in transcript number between 52,166 and 72,133 after quality filtering for low-read support transcripts (Table 1).
A number of SNPs fell into regions of alternative splicing such that the genomic placement of the SNP varied by transcript.
Since the time to splice is a distributed quantity, and splicing times vary from transcript to transcript, the variation in previously reported splicing rates may be strongly influenced by the temporal dynamic range of the method.
Generally, the transcription of the nine genes was lower in the flower vegetative organs (glumes, lemma, palea and lodicules), than in the male and female reproductive organs (stamens and pistil); however the absolute copy number of transcripts varied considerably.
Peak hIL-10 mRNA expression levels varied from 1.3 transcripts over HMBS in Ramos BL cells to 48 transcripts in Mutu-I BL cells.
The abundance and the relative ratio between these two transcripts varied with the growth phase, as the abundance of the longer transcript decreased when entering the stationary phase, whereas that of the shorter one increased at the same time.
Transcripts varied across mixtures, indicating that biological screening of whole water samples for potential estrogenicity may need to include alternative molecular pathways other than just steroid receptor binding.
Moreover, associated cellular functions of differentially regulated transcripts varied through the day in all investigated tissues.
Furthermore, the extent as well as relative increase or decrease in number of significantly regulated transcripts varied between time points and tissues.
