Summary of Study ST002077

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001317. The data can be accessed directly via it's Project DOI: 10.21228/M8GH6P This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002077
Study TitleDynamic Phaeodactylum tricornutum exometabolites
Study SummaryAlgal bacterial interactions in phycosphere microbial communities have important implications for the stability and productivity of algal biofuel systems, and algal metabolites are important mediators of those interactions. We characterized exometabolites and cell associated metabolites from the model diatom Phaeodactylum tricornutum across different growth stages.
Institute
Lawrence Livermore National Laboratory
Last NameBrisson
First NameVanessa
Address7000 East Ave, Livermore, CA, 94550, USA
Emailbrisson2@llnl.gov
Phone5107177560
Submit Date2022-02-02
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-08-18
Release Version1
Vanessa Brisson Vanessa Brisson
https://dx.doi.org/10.21228/M8GH6P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001317
Project DOI:doi: 10.21228/M8GH6P
Project Title:LLNL microBiospheres SFA
Project Summary:Algal and plant systems have the unrivaled advantage of converting solar energy and CO2 into useful organic molecules. Their growth and efficiency are largely shaped by the microbial communities in and around them. The microbiospheres Biospheres SFA seeks to understand phototroph-heterotroph interactions that shape productivity, robustness, the balance of resource fluxes, and the functionality of the surrounding microbiome.
Institute:Lawrence Livermore National Laboratory
Last Name:Brisson
First Name:Vanessa
Address:7000 East Ave, Livermore, CA, 94550, USA
Email:brisson2@llnl.gov
Phone:5107177560

Subject:

Subject ID:SU002160
Subject Type:Other organism
Subject Species:Phaeodactylum tricornutum

Factors:

Subject type: Other organism; Subject species: Phaeodactylum tricornutum (Factor headings shown in green)

mb_sample_id local_sample_id Type Time Point
SA1963131_extr-ctrl--extr-ctrl-_1extraction control extraction control
SA1963142_extr-ctrl--extr-ctrl-_2extraction control extraction control
SA1963154_extr-ctrl--extr-ctrl-_4extraction control extraction control
SA1963163_extr-ctrl--extr-ctrl-_3extraction control extraction control
SA1963179_exudate-0d_1exudate 0 days
SA19631811_exudate-0d_3exudate 0 days
SA19631910_exudate-0d_2exudate 0 days
SA19632012_exudate-0d_4exudate 0 days
SA19632128_exudate-12d_4exudate 12 days
SA19632225_exudate-12d_1exudate 12 days
SA19632326_exudate-12d_2exudate 12 days
SA19632427_exudate-12d_3exudate 12 days
SA19632514_exudate-3d_2exudate 3 days
SA19632613_exudate-3d_1exudate 3 days
SA19632716_exudate-3d_4exudate 3 days
SA19632815_exudate-3d_3exudate 3 days
SA19632920_exudate-6d_4exudate 6 days
SA19633018_exudate-6d_2exudate 6 days
SA19633119_exudate-6d_3exudate 6 days
SA19633217_exudate-6d_1exudate 6 days
SA19633324_exudate-9d_4exudate 9 days
SA19633423_exudate-9d_3exudate 9 days
SA19633522_exudate-9d_2exudate 9 days
SA19633621_exudate-9d_1exudate 9 days
SA1963375_exudate-med-ctrl-_1exudate medium control
SA1963386_exudate-med-ctrl-_2exudate medium control
SA1963397_exudate-med-ctrl-_3exudate medium control
SA1963408_exudate-med-ctrl-_4exudate medium control
SA19634134_pellet-0d_2pellet 0 days
SA19634236_pellet-0d_4pellet 0 days
SA19634335_pellet-0d_3pellet 0 days
SA19634433_pellet-0d_1pellet 0 days
SA19634550_pellet-12d_2pellet 12 days
SA19634649_pellet-12d_1pellet 12 days
SA19634751_pellet-12d_3pellet 12 days
SA19634852_pellet-12d_4pellet 12 days
SA19634940_pellet-3d_4pellet 3 days
SA19635038_pellet-3d_2pellet 3 days
SA19635139_pellet-3d_3pellet 3 days
SA19635237_pellet-3d_1pellet 3 days
SA19635344_pellet-6d_4pellet 6 days
SA19635443_pellet-6d_3pellet 6 days
SA19635542_pellet-6d_2pellet 6 days
SA19635641_pellet-6d_1pellet 6 days
SA19635747_pellet-9d_3pellet 9 days
SA19635848_pellet-9d_4pellet 9 days
SA19635946_pellet-9d_2pellet 9 days
SA19636045_pellet-9d_1pellet 9 days
SA19636129_pellet-med-ctrl-_1pellet medium control
SA19636231_pellet-med-ctrl-_3pellet medium control
SA19636330_pellet-med-ctrl-_2pellet medium control
SA19636432_pellet-med-ctrl-_4pellet medium control
Showing results 1 to 52 of 52

Collection:

Collection ID:CO002153
Collection Summary:Spent medium and cell pellets were collected from axenic Phaeodactylum tricornutum cultures at 5 time points: 0, 3, 6, 9, and 12 days after inoculation. Cultures from four replicate flasks were destructively harvested at each collection time point.
Sample Type:Algae

Treatment:

Treatment ID:TR002172
Treatment Summary:Treatments were different time points during algal growth: 0, 3, 6, 9, and 12 days after inoculation.

Sample Preparation:

Sampleprep ID:SP002166
Sampleprep Summary:Cell pellets were disrupted for metabolite extraction by resuspension in sterile water, lyophilization, and grinding by vortexing with a sterilized steel ball. Disrupted pellets were resuspended in 50 mL sterile water, filtered, and frozen in the same manner as spent medium. Spent medium and cell pellet samples were extracted by solid phase extraction using Agilent Bond Elut PPL columns.

Combined analysis:

Analysis ID AN003385 AN003386
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity
Column Agilent InfinityLab Poroshell 120 HILIC-Z (150 x 2.1mm,2.7um) Agilent InfinityLab Poroshell 120 HILIC-Z (150 x 2.1mm,2.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units metabolite quantification (peak height or area as denoted in metaboilite table) metabolite quantification (peak height or area as denoted in metaboilite table)

Chromatography:

Chromatography ID:CH002502
Instrument Name:Agilent 1290 Infinity
Column Name:Agilent InfinityLab Poroshell 120 HILIC-Z (150 x 2.1mm,2.7um)
Chromatography Type:HILIC

MS:

MS ID:MS003152
Analysis ID:AN003385
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolite identifications w ere obtained using Metabolite Atlas (https://github.com/biorack/metatlas) to identify features with m/z , retention time, and fragmentation spectra that matched to a library of analytical standards run in our lab under the same LC-MS/MS analysis conditions.
Ion Mode:POSITIVE
  
MS ID:MS003153
Analysis ID:AN003386
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolite identifications w ere obtained using Metabolite Atlas (https://github.com/biorack/metatlas) to identify features with m/z , retention time, and fragmentation spectra that matched to a library of analytical standards run in our lab under the same LC-MS/MS analysis conditions.
Ion Mode:NEGATIVE
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