cDNA Library and EST Characterization
| Riken embryo | Riken head | Adult testis | |
| Libraries | |||
| cDNA cloning vector | pFLC1 | pFLC1 | pOTB7 |
| PolyA presence | 100% (n = 485) | 92% (n = 352) | 99% (n = 445) |
| Inverted inserts[i] | 0% (n = 454) | 0% (n = 355) | 0.7% (n = 706) |
| Average insert length[ii] | 2.1 kb (n = 96) | 1.6 kb (n = 96) | 2.0 kb (n = 96) |
| Chimeric insert[iii] | <1% (n = 488) | 1.6% (n = 668) | 2.8% (n = 313) |
| Initial gene discovery rate[iv] | 10% | 9% | 23% |
| ESTs | |||
| Attempts | 71807 | 67870 | 29664 |
| Failed quality[v] | 10181 | 11731 | 6146 |
| Contaminant[vi] | 1372 | 1224 | 303 |
| Total high quality[vii] | 60254 | 54915 | 23215 |
| Average high quality read length | 484 | 472 | 528 |
[i] Determined by the presence of a polyA tract in the 5′-end sequence.
[ii] Determined by PCR amplification using primers in the cloning vector.
[iii] Clones whose 5′ and 3′ reads aligned to different chromosomal arms or >300 kb apart using Sim4.
[iv] Originally determined by pairwise Blast using all previous ESTs.
[v] Reads of <150 bp after vector and quality trimming.
[vi] Reads that were discarded because of significant hits to the Genbank GB.vector dataset.
[vii] See Methods for details.
[viii] EST, expressed sequence tag.