Dataset: RB-TnSeq Data

Name: Ruegeria pomeroyi RB-TnSeq Transponson Mutant Library Screen Experimental Data February 2021 (C-CoMP Marine Bacterial Transporters project)
Published: 2023-04-05
Keywords: RB-TnSeq, gene fitness, transporters, metabolism, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.893256.1

Temporal Extent: 2021-02 - 2021-02

Project:

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

Program:

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

Principal Investigator:

Mary Ann Moran (University of Georgia, UGA)

Co-Principal Investigator:

Christopher R. Reisch (University of Florida, UF)

Scientist:

Catalina Mejia (University of Florida, UF-SFRC)

Lidimarie Trujillo Rodriguez (University of Florida, UF)

Student:

William F. Schroer (University of Georgia, UGA)

Data Manager:

Laura Gray (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Sawyer Newman (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-04-05

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

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 the screen shows which mutants are enriched or depleted on each substrate, indicating the fitness advantage provided by each gene when grown on each substrate. This can indicate genes that are involved in the uptake and metabolism of each substrate.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2023-04-05	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.893256.1	2023-05-24

Data Processing Description

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 "_")

Data Files

File
rbtnseq_bcodmo_2.csv (Comma Separated Values (.csv), 1,014.10 KB) MD5:de395169ec8a3d2f6ffab393359813ba Primary data file for 893256. File processed with laminar pipeline "893256_v1_RB-TnSeq_Data" at path 893256/1/data/rbtnseq_bcodmo_2.csv

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2019589
Simons Foundation	542391

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: NextSeq SE150 (Illumina, San Diego, CA, USA)

Supplied Description:

An aliquot of 8 ng of product from each sample was pooled, purified using HiPrep beads (MagBio, Gaithersburg, MD, USA), and sequenced on a NextSeq SE150 Mid Output flow cell (SE150) at the Georgia Genomics and Bioinformatics Core Facility (Athens, Georgia, USA).

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

plate reader

Supplied Name: Synergy H1 plate reader (BioTek, Winooski, VT, USA)

Supplied Description:

After growth with shaking at 25oC for 72 h in a Synergy H1 plate reader (BioTek, Winooski, VT, USA) , cultures were serially transferred into fresh media four times and then transferred to 1.5 ml tubes, pelleted by centrifugation at 8,000 x g for 3 min, and stored at -80oC until further processing.

Instrument Type

Generic Name: plate reader

Generic Description:

Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Locus ID	Locus ID of a gene in the Ruegeria pomeroyi DSS-3 genome.	unitless	Site_ID
T0_1	Time 0 replicate 1	hours	time_sample
T0_2	Time 0 replicate 2	hours	time_sample
T0_3	Time 0 replicate 3	hours	time_sample
T0_4	Time 0 replicate 4	hours	time_sample
Cysteate_1	Replicate 1 sample grown on Cysteate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Cysteate_2	Replicate 2 sample grown on Cysteate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Cysteate_3	Replicate 3 sample grown on Cysteate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Cysteate_4	Replicate 4 sample grown on Cysteate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
DMSP_1	Replicate 1 sample grown on DMSP.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
DMSP_2	Replicate 2 sample grown on DMSP.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
DMSP_3	Replicate 3 sample grown on DMSP.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
DMSP_4	Replicate 4 sample grown on DMSP.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
DHPS_1	Replicate 1 sample grown on DHPS.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
DHPS_2	Replicate 2 sample grown on DHPS.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
DHPS_3	Replicate 3 sample grown on DHPS.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
DHPS_4	Replicate 4 sample grown on DHPS.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Leucine_1	Replicate 1 sample grown on Leucine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Leucine_2	Replicate 2 sample grown on Leucine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Leucine_3	Replicate 3 sample grown on Leucine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Leucine_4	Replicate 4 sample grown on Leucine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Arginine_1	Replicate 1 sample grown on Arginine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Arginine_2	Replicate 2 sample grown on Arginine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Arginine_3	Replicate 3 sample grown on Arginine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Arginine_4	Replicate 4 sample grown on Arginine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Ectoine_1	Replicate 1 sample grown on Ectoine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Ectoine_2	Replicate 2 sample grown on Ectoine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Ectoine_3	Replicate 3 sample grown on Ectoine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Ectoine_4	Replicate 4 sample grown on Ectoine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
GlcNAc_1	Replicate 1 sample grown on GlcNAc.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
GlcNAc_2	Replicate 2 sample grown on GlcNAc.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
GlcNAc_3	Replicate 3 sample grown on GlcNAc.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
GlcNAc_4	Replicate 4 sample grown on GlcNAc.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glucose_1	Replicate 1 sample grown on Glucose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glucose_2	Replicate 2 sample grown on Glucose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glucose_3	Replicate 3 sample grown on Glucose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glucose_4	Replicate 4 sample grown on Glucose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Xylose_1	Replicate 1 sample grown on Xylose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Xylose_2	Replicate 2 sample grown on Xylose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Xylose_3	Replicate 3 sample grown on Xylose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Xylose_4	Replicate 4 sample grown on Xylose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glycolate_1	Replicate 1 sample grown on Glycolate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glycolate_2	Replicate 2 sample grown on Glycolate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glycolate_3	Replicate 3 sample grown on Glycolate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glycolate_4	Replicate 4 sample grown on Glycolate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Phenylacetate_1	Replicate 1 sample grown on Phenylacetate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Phenylacetate_2	Replicate 2 sample grown on Phenylacetate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Phenylacetate_3	Replicate 3 sample grown on Phenylacetate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Phenylacetate_4	Replicate 4 sample grown on Phenylacetate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Malate_1	Replicate 1 sample grown on Malate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Malate_2	Replicate 2 sample grown on Malate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Malate_3	Replicate 3 sample grown on Malate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Malate_4	Replicate 4 sample grown on Malate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
3-Hydoxybutyrate_1	Replicate 1 sample grown on 3-Hydroxybutyrate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
3-Hydoxybutyrate_2	Replicate 2 sample grown on 3-Hydroxybutyrate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
3-Hydoxybutyrate_3	Replicate 3 sample grown on 3-Hydroxybutyrate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
3-Hydoxybutyrate_4	Replicate 4 sample grown on 3-Hydroxybutyrate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Acetate_1	Replicate 1 sample grown on Acetate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Acetate_2	Replicate 2 sample grown on Acetate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Acetate_3	Replicate 3 sample grown on Acetate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Acetate_4	Replicate 4 sample grown on Acetate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Spermidine_1	Replicate 1 sample grown on Spermidine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Spermidine_2	Replicate 2 sample grown on Spermidine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Spermidine_3	Replicate 3 sample grown on Spermidine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Spermidine_4	Replicate 4 sample grown on Spermidine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Threonine_1	Replicate 1 sample grown on Threonine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Threonine_2	Replicate 2 sample grown on Threonine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Threonine_3	Replicate 3 sample grown on Threonine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Threonine_4	Replicate 4 sample grown on Threonine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Tyramine_1	Replicate 1 sample grown on Tyramine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Tyramine_2	Replicate 2 sample grown on Tyramine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Tyramine_3	Replicate 3 sample grown on Tyramine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Tyramine_4	Replicate 4 sample grown on Tyramine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Gluconate_1	Replicate 1 sample grown on Gluconate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Gluconate_2	Replicate 2 sample grown on Gluconate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Gluconate_3	Replicate 3 sample grown on Gluconate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Gluconate_4	Replicate 4 sample grown on Gluconate.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Serine_1	Replicate 1 sample grown on Serine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Serine_2	Replicate 2 sample grown on Serine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Serine_3	Replicate 3 sample grown on Serine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Serine_4	Replicate 4 sample grown on Serine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glycine_1	Replicate 1 sample grown on Glycine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glycine_2	Replicate 2 sample grown on Glycine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glycine_3	Replicate 3 sample grown on Glycine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Glycine_4	Replicate 4 sample grown on Glycine.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Ribose_1	Replicate 1 sample grown on Ribose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Ribose_2	Replicate 2 sample grown on Ribose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Ribose_3	Replicate 3 sample grown on Ribose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Ribose_4	Replicate 4 sample grown on Ribose.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Proline_1	Replicate 1 sample grown on Proline.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Proline_2	Replicate 2 sample grown on Proline.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Proline_3	Replicate 3 sample grown on Proline.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
Proline_4	Replicate 4 sample grown on Proline.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
IAM_1	Replicate 1 sample grown on IAM.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
IAM_2	Replicate 2 sample grown on IAM.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
IAM_3	Replicate 3 sample grown on IAM.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate
IAM_4	Replicate 4 sample grown on IAM.	Number of sequence counts (barcodes) that mapped to each gene in the treatment.	replicate

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Dataset: RB-TnSeq Data