Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

6.2 Tag mapping Results
ent analyses. We first mapped all the tags obtained from the process described
in fig 6.2 to known transcripts, then we mapped the remaining tags to cDNA
libraries. Finally, we mapped the remaining tags to the genome for the poten-
tial discovery of new unannotated transcripts. As a result of this strategy, we
collected in "Ref_uniq" - our most stringent set - all the tags mapping to a
single reference gene and in "Ref_best" - our second most stringent set - all
the tags included in the former with the addition of tags mapping to multiple
genes of which, however, only one was a reference transcript. The conservative
set of tag-to-transcript mappings ("Ref_uniq") comprised 25,593 unique tags
assigned to 15,103 genes, and formed our primary dataset for further anal-
ysis. In addition, we created several more comprehensive tag mapping sets,
by including mappings to other cDNA sequences, expressed sequence tags,
internal NlaIII sites and unannotated genomic regions ("cDNA_uniq" and
"cDNA_best").
Figure 6.4: Diagram of the tag mapping strategy where each filtered tag is assigned
to a more or less stringent set used for future analyses.
As shown in figure 6.5, on average more than 55% of tags (green) in every cell
line could not be classified as belonging to any of the sets identified with the
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