Up to 5.0 mg of cDNA or genomic DNA was subjected directly to preparation of 454-DNA libraries and subsequently to pyrosequencing without any prior PCR or cloning steps. Library preparation and pyrosequencing were performed as described previously [60] on a Roche GS20 sequencer FLX (Roche Applied Sciences/454 Life Sciences, Branford, CT), producing sets of RNA-tags or DNA-tags, respectively. The runs were performed on either quarter or half plates, resulting in read numbers between 10,673 and 176,878 and base numbers in the range of 1,411,420 to 41,066,808. The MD OCT-pool cDNA library was run twice due to low read and base numbers of the first run, and the transcript-tags of these two runs and of the run following the normalization approach (see above) were combined for all subsequent data analysis. Sequences are deposited to the Sequence Read Archive (in progress).