A comparative analysis of the information content in long and short SAGE libraries

BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a powerful tool to determine gene expression profiles. Two types of SAGE libraries, ShortSAGE and LongSAGE, are classified based on the length of the SAGE tag (10 vs. 17 basepairs). LongSAGE libraries are thought to be more useful than ShortSAGE libraries, but their information content has not been widely compared. To dissect the differences between these two types of libraries, we utilized four libraries (two LongSAGE and two ShortSAGE libraries) generated from the hippocampus of Alzheimer and control samples. In addition, we generated two additional short SAGE libraries, the truncated long SAGE libraries (tSAGE), from LongSAGE libraries by deleting seven 5' basepairs from each LongSAGE tag. RESULTS: One problem that occurred in the SAGE study is that individual tags may have matched to multiple different genes – due to the short length of a tag. We found that the LongSAGE tag maps up to 15 UniGene clusters, while the ShortSAGE and tSAGE tags map up to 279 UniGene clusters. Both long and short SAGE libraries exhibit a large number of orphan tags (no gene information in UniGene), implying the limitation of the UniGene database. Among 100 orphan LongSAGE tags, the complete sequences (17 basepairs) of nine orphan tags match to 17 genomic sequences; four of the orphan tags match to a single genomic sequence. Our data show the potential to resolve 4–9% of orphan LongSAGE tags. Finally, among 400 tSAGE tags showing significant differential expression between AD and control, 79 tags (19.8%) were derived from multiple non-significant LongSAGE tags, implying the false positive results. CONCLUSION: Our data show that LongSAGE tags have high specificity in gene mapping compared to ShortSAGE tags. LongSAGE tags show an advantage over ShortSAGE in identifying novel genes by BLAST analysis. Most importantly, the chances of obtaining false positive results are higher for ShortSAGE than LongSAGE libraries due to their specificity in gene mapping. Therefore, it is recommended that the number of corresponding UniGene clusters (gene or ESTs) of a tag for prioritizing the significant results be considered

An Exploratory Sequential Mixed Methods Approach to Understanding Researchers’ Data Management Practices at UVM: Findings from the Qualitative Phase

The objective of this article is to report on the first qualitative phase of an exploratory sequential mixed methods research design focused on researcher data management practices and related institutional research data services. The aim of this study is to understand data management behaviors of faculty at the University of Vermont (UVM), a higher-research activity Research University, in order to guide the development of campus research data management services. The population of study was all faculty who received National Science Foundation (NSF) grants between 2011 and 2014 who were required to submit a data management plan (DMP); qualitative data was collected in two forms: (1) semi-structured interviews and (2) document analysis of data management plans. From a population of 47 researchers, six were included in the interview sample, representing a broad range of disciplines and NSF Directorates, and 35 data management plans were analyzed. Three major themes were identified through triangulation of qualitative data sources: data management activities, including data dissemination and data sharing; institutional research support and infrastructure barriers; and perceptions of data management plans and attitudes towards data management planning. The themes articulated in this article will be used to design a survey for the second quantitative phase of the study, which will aim to more broadly generalize data management activities at UVM across all disciplines

XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis

BACKGROUND: Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have analyzed 350,468 Xenopus laevis Expressed Sequence Tags (ESTs) both to identify full length protein encoding sequences and to develop a unique database system to support comparative approaches between X. laevis and other model systems. DESCRIPTION: Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences. Generation of a consensus sequence for each cluster resulted in 31,353 tentative contig and 4,801 singleton sequences. Using both BLASTX and FASTY comparison to five model organisms and the NR protein database, more than 15,000 sequences are predicted to encode full length proteins and these have been matched to publicly available IMAGE clones when available. Each sequence has been compared to the KOG database and ~67% of the sequences have been assigned a putative functional category. Based on sequence homology to mouse and human, putative GO annotations have been determined. CONCLUSION: The results of the analysis have been stored in a publicly available database XenDB . A unique capability of the database is the ability to batch upload cross species queries to identify potential Xenopus homologues and their associated full length clones. Examples are provided including mapping of microarray results and application of 'in silico' analysis. The ability to quickly translate the results of various species into 'Xenopus-centric' information should greatly enhance comparative embryological approaches. Supplementary material can be found at

An Exploratory Sequential Mixed Methods Approach to Understanding Researchers’ Data Management Practices at UVM: Integrated Findings to Develop Research Data Services

This article reports on the integrated findings of an exploratory sequential mixed methods research design aimed to understand data management behaviors and challenges of faculty at the University of Vermont (UVM) in order to develop relevant research data services. The exploratory sequential mixed methods design is characterized by an initial qualitative phase of data collection and analysis, followed by a phase of quantitative data collection and analysis, with a final phase of integration or linking of data from the two separate strands of data. A joint display was used to integrate data focused on the three primary research questions: How do faculty at UVM manage their research data, in particular how do they share and preserve data in the long-term?; What challenges or barriers do UVM faculty face in effectively managing their research data?; and What institutional data management support or services are UVM faculty interested in? As a result of the analysis, this study suggests four major areas of research data services for UVM to address: infrastructure, metadata, data analysis and statistical support, and informational research data services. The implementation of these potential areas of research data services is underscored by the need for cross-campus collaboration and support

Evaluating Digital Libraries: A Longitudinal and Multifaceted View

published or submitted for publicatio

Evaluating the strategic plans of public libraries : an inspection-based approach

For public libraries, as with most organisations, effective strategic planning is critical to longevity, facilitating cohesive and coordinated responses to ever present and ever changing political, economic, social, and technological (PEST) forces which shape and influence direction. However, strategic planning is widely recognised as a challenging activity, which can be both time consuming and unproductive, and there exists limited guidance regarding how to evaluate documented and disseminated strategic plans, particularly within the not-for-profit sector. In response, this research proposes and tests an inspection-based approach to the evaluation of strategic plans, based upon a rubric specifying the key attributes of each of the core components of a plan, combined with an appropriate assessment scale. The rubric provides a method to identify and assess completeness of strategic plan, extending to qualitative assessment of communication aspects such as specification and terminology, and synergistic aspects such as cohesion and integration. The method is successfully trialled across the devolved Scottish public library sector with the strategic plans of 28 of the 32 regional networks evaluated. 17 of 28 plans (61%) were found to be incomplete and/or to contain contradictory or uncoordinated components, with it recommended that Scottish public libraries improve not only completeness of plans, but also their precision, specificity, explicitness, coordination, and consistency, and overall mapping to library services. Recommendations are made for further widespread application of the rubric

Problems and Promises of Using LMS Learner Analytics for Assessment: Case Study of a First-Year English Program

Learning management systems (LMS) are widely used in education. They offer the potential for assessing student learning, but the reality of using them for this is problematic. This case study chronicles efforts by librarians at Marquette University to use LMS data to assess students’ information literacy knowledge in Marquette’s first-year English program

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.

As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics