Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia

We report the construction of the mouse full-length cDNA encyclopedia, the most extensive view of a complex transcriptome, on the basis of preparing and sequencing 246 libraries. Before cloning, cDNAs were enriched in full-length by Cap-Trapper, and in most cases, aggressively subtracted/normalized. We have produced 1,442,236 successful 3'-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5' end reads, which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU), which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC), which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large. numbers of clusters (and TUs) of this project, which also include non-protein-coding RNAs, and the lower gene number estimation of genome annotations. Altogether, S'-end clusters identify regions that are potential promoters for 8637 known genes and S'-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.

A total electron content space weather study of the Nighttime Weddell Sea Anomaly of 1996/97 southern summer with TOPEX/Poseidon radar altimetry

This paper reports on a total electron content space weather study of the nighttime Weddell Sea Anomaly, overlooked by previously published TOPEX/Poseidon climate studies, and of the nighttime ionosphere during the 1996/1997 southern summer. To ascertain the morphology of spatial TEC distribution over the oceans in terms of hourly, geomagnetic, longitudinal and summer-winter variations, the TOPEX TEC, magnetic, and published neutral wind velocity data are utilized. To understand the underlying physical processes, the TEC results are combined with inclination and declination data plus global magnetic field-line maps. To investigate spatial and temporal TEC variations, geographic/magnetic latitudes and local times are computed. As results show, the nighttime Weddell Sea Anomaly is a large (∼1,600(°)2; ∼22 million km2 estimated for a steady ionosphere) space weather feature. Extending between 200°E and 300°E (geographic), it is an ionization enhancement peaking at 50°S–60°S/250°E–270°E and continuing beyond 66°S. It develops where the spacing between the magnetic field lines is wide/medium, easterly declination is large-medium (20°–50°), and inclination is optimum (∼55°S). Its development and hourly variations are closely correlated with wind speed variations. There is a noticeable (∼43%) reduction in its average area during the high magnetic activity period investigated. Southern summer nighttime TECs follow closely the variations of declination and field-line configuration and therefore introduce a longitudinal division of four (Indian, western/eastern Pacific, Atlantic). Northern winter nighttime TECs measured over a limited area are rather uniform longitudinally because of the small declination variation. TOPEX maps depict the expected strong asymmetry in TEC distribution about the magnetic dip equator.