Table 1.
Overview of the Number of cDNA Clones Analyzed, Normalized by Oligonucleotide Fingerprinting and Sequenced Across Various Libraries That Represent the Different Developmental Stages
| Stage | EGC | Cleavage | Blastula | Gastrula | Larva | Total |
|---|---|---|---|---|---|---|
| Clones analyzed by ONF | 6291 | 10,368 | 18,432 | 18,432 | 53,760 | 107,283 |
| Clones included in ONF clustering | 4689 | 9375 | 16,925 | 15,617 | 44,786 | 91,392 |
| Normalized in ONF clustering | 3098 1.5-fold | 4069 2.3-fold | 6557 2.6-fold | 6635 2.3-fold | 14,877 3.0-fold | 35,238 2.6-fold |
| Clones remaining as singletons (%) | 2673 (57%) | 3392 (36%) | 5421 (32%) | 5774 (37%) | 13,044 (29%) | 30,304 (33%) |
| Clones selected for sequencing | 6291 | 4091 | 6650 | 6659 | 15,746 | 39,437 |
| Total number of sequence reads | 6126 | 5546 | 9974 | 8095 | 12,968 | 42,709 |
| Number of 5′ reads | 6126 (100%) | 2894 (52.2%) | 5270 (52.8%) | 5604 (69.2%) | 10,575 (81.5%) | 30,469a (71.3%) |
| Number of 3′ reads | 0 | 2652 (47.8%) | 4704 (47.2%) | 2491 (30.8) | 2491 (18.5%) | 12,240 (28.7%) |
As an internal control, the nonredundant 6291 clones that were previously normalized from an unfertilized egg cDNA library (Poustka et al. 1999) were again subjected to ONF analysis. cDNA clones that were clustered together with those clones previously sequenced from the unfertilized egg cDNA library were rejected from sequencing because these transcripts were already identified. A total of 4689 of the unfertilized egg cDNA clones were included in the cluster analysis. If those were clustered again, they were assembled into 4098 clusters. This is a reduction in redundancy by only 12%, indicating the high normalization rate that can be achieved by ONF.
This number is equal to the total number of different clones sequenced