Dataset - Transcriptomics, Sequencing Serine recombinase assisted genome engineering, relative transcriptional profiling (SAGE-RTP)

Data Sample

PRJNA841687_BioSamples_15.txt
Scientific Discovery
Biology
Microbiome Science
PerCon SFA
Synthetic Biology
Amplicon Sequencing
DNA Barcode Abundances
Statistical Expression Analysis
R. jostii RHA1
P. putida GPO1
R. palustris CGA009
P. frederiksbergensis TBS10
P. fluorescens SBW25

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

    • NCBI BioProject: PRJNA841687 (15 BioSamples; 120 raw sequence reads)

    Related Organisms

    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. 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
    2. 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. 

    Data Reuse Citation Policy

    When referencing and reusing linked PerCon SFA project digital data assets listed at the PNNL DataHub institutional repository, we ask that users please cite the dataset digital object identifier provided at the download page and any corresponding journal article publications. Reference citations, where applicable, should provide the necessary metadata information required to support, corroborate, verify, and otherwise determine the legitimacy of the research findings provided (data and code) from scholarly publications and corresponding project data releases.

      Data Licensing

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

      English
      Projects (1)
      Persistence Control of Engineered Functions in Complex Soil Microbiomes (PerCon SFA), Secure Biosystems Design Project
      Publications (1)
      High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration
      People (3)
      Lindsey N. Anderson

      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...

      Joshua Elmore

      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...

      Robert Egbert

      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...

      Data Sources (1)
      Illumina HiSeq 4000 Sequencing System