Serine recombinase assisted genome engineering, relative transcriptional profiling (SAGE-RTP) (PRJNA841687)

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Description

Last updated on 2023-03-21T18:35:22+00:00 by LN Anderson

SAGE-RTP RT-PCR Amplicon Sequencing Barcode Count Analysis

Promoter expression data for five bacterial species associated with the Serine recombinase Assisted Genome Engineering (SAGE) research project.

    Raw Measurement Data

    Reference Taxonomy

    1. Rhodopseudomonas palustris CGA009 [NCBITAXON:258594]
    2. Pseudomonas putida (GPO1) [NCBITAXON:303]
    3. Rhodococcus jostii (RHA1) [NCBITAXON:132919]
    4. Pseudomonas frederiksbergensis (TBS10) [NCBITAXON:104087]
    5. Pseudomonas fluorescens (SBW25) [NCBITAXON:294]

    Reference Citations

    1. Pacific Northwest National Laboratory. Raw sequencing reads for relative transcriptional profiling (RTP) experiments associated with the Serine recombinase Assisted Genome Engineering (SAGE) research project. 2022/05. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA841687. NCBI:BioProject: PRJNA841687.
    2. Elmore JR, Dexter GN, Baldino H, Huenemann JD, Francis R, Peabody GL 5th, Martinez-Baird J, Riley LA, Simmons T, Coleman-Derr D, Guss AM, Egbert RG. High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration. Sci Adv. 2023 Mar 10;9(10):eade1285. doi: https://doi.org/10.1126/sciadv.ade1285
    3. Robert G. Egbert, & Joshua R. Elmore. (2022). Serine Recombinase-Assisted Genome Engineering - Relative Transcriptional Profiling (SAGE-RTP) Toolkit (1.0). Zenodo. https://doi.org/10.5281/zenodo.7388406

     

    Funding Acknowledgments

    The provided material is based upon work supported by the  U.S. Department of Energy, Office of Biological and Environmental Research, Genomic Science Program and is a contribution of the Pacific Northwest National Laboratory Persistence Control of Engineered Functions in Complex Soil Microbiomes project. Pacific Northwest National Laboratory is a multiprogram national laboratory managed by the Battelle Memorial Institute Battelle Memorial Institute, operating under the U.S. Department of Energy Contract DE-AC05-76RL01830. 

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      Data Licensing

      CC BY-SA 4.0 (processed datasets), CC0 1.0 PNNL DataHub policy default for metadata)

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      Lindsey Anderson’s research has been dedicated to the identification and characterization of novel, targeted and non-targeted, functional metabolic interactions using a high-throughput systems biology and computational biology approach. Her expertise in functional metabolism and multidisciplinary...

      Dr. Joshua Elmore is a Chemical Engineer at Pacific Northwest National Laboratory. He received his Ph. D. from the University of Georgia in the Department of Molecular Biology and Biochemistry studying the mechanisms of CRISPR/Cas microbial immune systems in hyperthermophilic Archaea. He was a...

      Biography I am a biological engineer working to advance high-throughput biological engineering for rapid optimization of complex gene clusters and dynamical systems in microbes through pooled genomic library assembly, high-throughput sequencing and variant scoring. I utilize machine learning...

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