Dataset: Ruegeria pomeroyi RB-TnSeq Transponson Mutant Library Screen Experimental Data February 2021 (C-CoMP Marine Bacterial Transporters project)

Final no updates expectedDOI: 10.26008/1912/bco-dmo.893256.1Version 1 (2023-04-05)Dataset Type:experimental

Principal Investigator: Mary Ann Moran (University of Georgia)

Co-Principal Investigator: Christopher R. Reisch (University of Florida)

Scientist: Catalina Mejia (University of Florida)

Scientist: Lidimarie Trujillo Rodriguez (University of Florida)

Student: William F. Schroer (University of Georgia)

Data Manager: Laura Gray (Woods Hole Oceanographic Institution)

BCO-DMO Data Manager: Sawyer Newman (Woods Hole Oceanographic Institution)

Program: Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Project: Function and Importance of Marine Bacterial Transporters of Plankton Exometabolites (C-CoMP Marine Bacterial Transporters)

Abstract

A barcoded transposon mutant library (RB-TnSeq) of Ruegeria pomeroyi DSS-3 was screened on 23 substrates, each as a sole carbon source. In February of 2021 the RB-TnSeq library was grown in the laboratory in minimal medium with a substrate of interest, cultures were sequentially transfered four times to increase selection. Mutants with phenotypes that decreased fitness on the substrate of interest grow at a lower rate than mutants with no loss of fitness. Sequencing the barcodes of mutants after...

Show more
Cite Dataset

Processing Notes from Researcher:

Sequence data were processed according to Wetmore et al (2015). Following quality control, an average of 35,090 unique barcodes mapped to insertions that fell within the interior 10 to 90% of R. pomeroyi coding sequences. In total, 55 million reads were mapped to insertions in 3,570 genes (out of 4,469 protein-encoding genes in the R. pomeroyi genome) with a median of 404,513 mapped reads per sample. Reads mapping to different insertion sites within the same coding sequence were pooled.

BCO-DMO Processing Notes:

  • Removed spaces and special characters from column header names (replaced with underscores "_")

 

 

Related Datasets

No Related Datasets

Related Publications

Results
Schroer, W. F., Kepner, H. E., Uchimiya, M., Mejia, C., Rodriguez, L. T., Reisch, C. R., & Moran, M. A. (2023). Function and Importance of Marine Bacterial Transporters of Plankton Exometabolites. https://doi.org/10.1101/2023.01.19.524783
Results
Schroer, W. F., Kepner, H. E., Uchimiya, M., Mejia, C., Rodriguez, L. T., Reisch, C. R., & Moran, M. A. (2023). Functional annotation and importance of marine bacterial transporters of plankton exometabolites. ISME Communications, 3(1). https://doi.org/10.1038/s43705-023-00244-6
Methods
Wetmore, K. M., Price, M. N., Waters, R. J., Lamson, J. S., He, J., Hoover, C. A., Blow, M. J., Bristow, J., Butland, G., Arkin, A. P., & Deutschbauer, A. (2015). Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons. MBio, 6(3). https://doi.org/10.1128/mbio.00306-15

Moran, M. A., Reisch, C. R., Mejia, C., Trujillo Rodriguez, L. (2023) Ruegeria pomeroyi RB-TnSeq Transponson Mutant Library Screen Experimental Data February 2021 (C-CoMP Marine Bacterial Transporters project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-04-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.893256.1 [access date]

Terms of Use

This dataset is licensed under Creative Commons Attribution 4.0.


If you wish to use this dataset, it is highly recommended that you contact the original principal investigators (PI). Should the relevant PI be unavailable, please contact BCO-DMO (info@bco-dmo.org) for additional guidance. For general guidance please see the BCO-DMO Terms of Use document.

NSF Logo©2020 Biological and Chemical Oceanography Data Management Office.
Funded by the U.S. National Science Foundation