While it is possible that the changes in transcript levels reflect alterations in the relative representation of myeloid cell populations, we think rather that they resulted at least partially from gene induction or repression because they were so rapid and because only a fraction of the transcript set characteristic of any particular cell-type showed an altered level of expression.
Because many of the transcripts were represented by multiple probe sets, the actual number of genes differentially expressed in AA astrocytes compared to CA astrocytes was 87.
We decided to use stop to stop because many of the transcripts were partial, and did not expect to see a methionine in these cases.
Because some of the transcripts were determined to be differentially expressed using qRT-PCR, it is clear that a number of differentially-regulated transcripts were missed from the cDNA-AFLP analysis, probably due to short-comings of the method itself.
Considering CiFT, we did not obtain very clear signals at these stages (data not shown), possibly because of low abundance of the transcript.
We were unable, however, to quantitate ABCC6P2 expression levels by real-time PCR because the small size of the transcript and its exceedingly high sequence homology with ABCC6 and ABCC6P1 hampered specific detection of ABCC6P2 mRNA.
On the other hand, we could not reliably annotate a high proportion of unigenes lacking assignment of a putative function because they did not cover the full length of the transcript or because they represent untranslated regions.
Also, it is possible that many TCs and sESTs could not be reliably annotated because they did not cover the entire length of the transcript or because they represent untranslated regions (UTRs).
Transcription of the pyr operon was verified by dot blot analysis because of the large transcript expected, using a pyrP-specific probe (data not shown).
SOUL was first identified at the transcriptional level by suppression subtractive hybridization in the chicken retina and pineal gland, and its gene was named ckSoul because of the high transcript levels found in the pineal gland, the organ René Descartes hypothesized was the location of the soul [ 15].
