Next-generation sequencing is excellently suited to evaluate the abundance of mRNAs to study gene expression. Here we compare two alternative technologies, cap analysis of gene expression (CAGE) and serial analysis of gene expression (SAGE), for the same RNA samples. Along with quantifying gene expression levels, CAGE can be used to identify tissue-specific transcription start sites, while SAGE...

Short-tooth sage (Salvia brachyodon Vandas) is an endemic and one of the rarest plant species of the Dinaric karst. Although older literature indicates its presence in more localities, only two have been confi rmed at the present time, Mt. Orjen (border of Bosnia and Herzegovina and Montenegro) and Pelješac peninsula (Croatia). Due to its very narrow distribution and economically very interesti...

—Anthropogenic noise can limit the ability of birds to communicate by masking their acoustic signals. Masking, which reduces the distance over which the signal can be perceived by a receiver, is frequency dependent, so the different notes of a single song may be masked to different degrees. We analyzed the individual notes of mating vocalizations produced by Greater Sage-Grouse (Centrocercus ur...

Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of gene expression (SAGE) can reveal new Poly(A) RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites i...

Serial Analysis of Gene Expression (SAGE) is a powerful expression profiling method, allowing the analysis of the expression of thousands of transcripts simultaneously. A disadvantage of the method, however, is the relatively high amount of input RNA required. Consequently, SAGE cannot be used for the generation of expression profiles when RNA is limited, i.e. in small biological samples such a...

This is a preliminary report on a project to characterize the historic species composition of coastal sage scrub vegetation in southern California using plot data collected between 1929 and 1934 by the USDA Forest Service's Vegetation Type Map (VTM) survey. Records and maps from a large historic data set collected for the VTM survey were converted into a digital database and GIS coverage. Histo...

This paper describes Sage, a software environment supporting software development, synthesis, and testing for distributed computing applications. While the principal domain of interest is applications that must be fault-tolerant (i.e., be able to withstand the failure of some of the participants) Sage is not limited to this; it can be extended to distributed applications with no criticality req...

Human land use, such as livestock grazing, can have profound yet varied effects on wildlife interacting within common ecosystems, yet our understanding of land-use effects is often generalized from short-term, local studies that may not correspond with trends at broader scales. Here we used public land records to characterize livestock grazing across Wyoming, USA, and we used Greater Sage-grous...

MOTIVATION SAGE (Serial Analysis of Gene Expression) can be used to estimate the number of unique transcripts in a transcriptome. A simple estimator that corrects for sequencing and sampling errors was applied to a SAGE library (137 832 tags) obtained from mouse embryonic stem cells, and also to Monte Carlo simulated libraries generated using assumed distributions of 'true' expression levels co...