Patterns of variation can be tissue specific or shared across multiple tissues and transcripts can vary between tissue samples collected from the same animal.
The early biosynthetic genes, TaCPS, TaKS, TaKO and TaKAO, and the signalling genes TaRht, TaGID1 and TaGID2, are expressed at all stages of development, albeit with marked variation in transcript levels between tissues and stages.
NMD efficiency is known to vary greatly between transcripts, tissues and individuals and it is possible that differences in survival of PTC-containing transcripts partially explain the striking phenotypic variability that characterizes ZIC3-associated congenital defects.
Next, we investigated the association between metabolites and transcripts in each tissue separately across the 16 pigs (see methods above).
This dendrogram resembles similar constructs built from coding transcript expression data [ 31], indicating that transcripts containing HERV-W gag elements vary between tissues similarly to such transcripts.
Notably, none of the transcripts was shared between somatic/gonadal tissues and spermatozoa.
It is not clear why there should be differential expression of the mitochondrial transcriptome between tissues with higher abundance of transcripts in gill and digestive gland than mantle and foot but this may reflect different physiological roles of the tissues and different energy demands.
Transcript up- and down-regulation differed strongly between the tissues and showed sensitivity to the time of day (Fig. 1).
We counted from 45,000 to 48,000 transcripts from 3 tissues and compared the transcriptional levels between each pair of tissues.
However, we found, through an extensive expression analysis of OsSUT genes, that the transcripts for OsSUT3 and OsSUT5 were extremely low or undetectable in mature leaf blades of rice and that the transcript levels of OsSUT4 were much lower than those of OsSUT1 and did not differ between mesophyll tissues and vascular bundle (Additional file 3: Figure S2; also see Aoki et al. [2003]).
