Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency

Table 1 Annotation-based filtering of candidate novel and intergenically spliced PET-based TUs.

Selection process	Initial dataset	Genomic span > 200 kb	Halftag/s within repeats	Mapping to multiple loci	Unmappable to the genome	No longer novel	Final PETs
Novel	143	48	48	26	10	1	10
Intergenic Splicing	10	-	-	-	3	1	6
Total	153	48	48	26	13	2	16

The numbers refer to PET counts in each named category corresponding to annotation-based filtering described in the text. The 'Mapping to multiple loci' and 'Unmappable to the genome' columns are the combined results of both In-Silico PCR and BLASTN.

ISSN: 1471-2164