Nonselected Candidate Genes Engineered by the BioEnergy Science Center: 2007-2012

Data table with downloadable file and more information.

Nelson, R.S., Stewart Jr., C.N., Gou, J., Holladay, S., Gallego-Giraldo, L., Flanagan, A., Mann, D.G.J., Hisano, H., Wuddineh, W.A., Poovaiah, C.R., Srivastava, A., Biswal, A.K., Shen, H., Escamilla-Trevino, L.L., Yang, J., Hardin, C.F., Nandakumar, R., Fu, C., Zhang, J., Xiao, X., Percifield, R., Chen, F., Bennetzen, J.L., Udvardi, M., Mazarei, M., Dixon, R.A., Wang, Z.Y., Tang, Y., Mohnen, D., Davison, B.H., "Development and use of a switchgrass (Panicum virgatum L.) transformation pipeline by the BioEnergy Science Center to evaluate plants for reduced cell wall recalcitrance", Biotechnology for Biofuels, 10:309, 2017. DOI: 10.1186/s13068-017-0991-x

Genome-Wide Association Study (GWAS) Dataset Released

Includes genotype origin and SNP calls per genotype for ca. 1000 Populus trichocarpa genotypes.

Downloadable file and more information.

This resource provides access to several types of BESC related datasets. These include the current list of BESC publications with direct links to data submissions (by Accession numbers) in public repositories (e.g. NCBI, PDB, ATCC). Also included is an interactive mode of exploration of multi-level BESC omics data (genome, transcriptome, proteome), using the JBrowse genome browser.

BESC Data in Public Repositories

Links to BESC data submissions in public repositories (e.g. NCBI, PDB, ATCC), in support of BESC publications.

Genome Data Exploration using JBrowse

We provide genome-centric exploration of multi-level omics data (genome, transcriptome, proteome) under genome browser environment. We have done this via JBrowse, a recent successor to the popular GBrowse generic genome browser software. It is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. JBrowse facilitates fast, smooth exploration of multi-gigabase genomes and associated features.

BESC Genomes

Note: The links below will open up a JBrowse instance in a new window. Browser support for JavaScript required. We are working to fix occasional problems encountered when using some versions of Internet Explorer.

Genome Description
Clostridium thermocellum DSM 1313 Analysis of genetic variation from different lineage samples from metabolic engineering of Clostridium thermocellum DSM 1313
Clostridium thermocellum ATCC 27405 Identified promoter regions by 5' Race RNA-Sequencing of Clostridium thermocellum ATCC 27405 for transcription unit architecture
Populus trichocarpa 210_v3 Omics Integration of genetic variation at DNA and RNA level, gene expression and proteomics analysis of different genotypes of Poplar trichocarpia

See also BESC related tools

BioEnergy Science Center 2007-2017