Summary of Study ST002154

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 PR001367. The data can be accessed directly via it's Project DOI: 10.21228/M8170M 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 IDST002154
Study TitleVirus-host interaction studies of P. plecoglossicida strain (NZBD9) and Epinephelus coioides.
Study SummaryE. coioides of the infection group were intrapleurally injected with 105 colony-forming units per fish (cfu/fish) of P. plecoglossicida (wild-type strain or clpV-RNAi strain), while control E. coioides received an equivalent volume of phosphate-buffered saline (PBS). The temperature of the water was maintained at 18 ± 1 °C during the infection experiment. The spleens of E. coioides were collected at 6, 12, 24, 48, 72 and 96 hours post injection (hpi).
Institute
Jimei University
Last NameYang
First NameZhiqiang
AddressNo. 185 Yinjiang Road, Jimei District, Xiamen City, Fujian Province, No. 185 Yinjiang Road
Email201911832016@jmu.edu.cn
Phone5926181487
Submit Date2022-04-09
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-05-16
Release Version1
Zhiqiang Yang Zhiqiang Yang
https://dx.doi.org/10.21228/M8170M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001367
Project DOI:doi: 10.21228/M8170M
Project Title:Metabolomics Insights into the Interaction between Pseudomonas plecoglossicida and Epinephelus coioides
Project Summary:Here, a P. plecoglossicida strain (NZBD9) and economic fish of Epinephelus coioides were investigated as a model system to characterize pathogen-induced host metabolic remodeling over the course of infection. We present a nontargeted metabolomics profiling of E. coioides spleens from uninfected E. coioides and those infected with wild-type and clpV-RNA interference (RNAi) strains.
Institute:College of Marine Food and Biological Engineering, Jimei University
Laboratory:Xiamen Key Laboratory of Marine Functional Food, Xiamen 361021, China
Last Name:Yang
First Name:Zhiqiang
Address:No. 185 Yinjiang Road, Jimei District, Xiamen City, Fujian Province, China
Email:201911832016@jmu.edu.cn
Phone:86-592-6181487

Subject:

Subject ID:SU002240
Subject Type:Fish
Subject Species:Epinephelus coioides

Factors:

Subject type: Fish; Subject species: Epinephelus coioides (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA206457clpv2d-5clpV-RNAi strain infection group
SA206458clpv2d-6clpV-RNAi strain infection group
SA206459clpv2d-7clpV-RNAi strain infection group
SA206460clpv3d-1clpV-RNAi strain infection group
SA206461clpv2d-4clpV-RNAi strain infection group
SA206462clpv2d-3clpV-RNAi strain infection group
SA206463clpv1d-7clpV-RNAi strain infection group
SA206464clpv2d-1clpV-RNAi strain infection group
SA206465clpv2d-2clpV-RNAi strain infection group
SA206466clpv3d-2clpV-RNAi strain infection group
SA206467clpv3d-3clpV-RNAi strain infection group
SA206468clpv4d-3clpV-RNAi strain infection group
SA206469clpv4d-4clpV-RNAi strain infection group
SA206470clpv4d-5clpV-RNAi strain infection group
SA206471clpv4d-6clpV-RNAi strain infection group
SA206472clpv4d-2clpV-RNAi strain infection group
SA206473clpv4d-1clpV-RNAi strain infection group
SA206474clpv3d-4clpV-RNAi strain infection group
SA206475clpv3d-6clpV-RNAi strain infection group
SA206476clpv3d-7clpV-RNAi strain infection group
SA206477clpv1d-6clpV-RNAi strain infection group
SA206478clpv1d-5clpV-RNAi strain infection group
SA206479clpv6-5clpV-RNAi strain infection group
SA206480clpv6-6clpV-RNAi strain infection group
SA206481clpv6-7clpV-RNAi strain infection group
SA206482clpv12-1clpV-RNAi strain infection group
SA206483clpv6-4clpV-RNAi strain infection group
SA206484clpv6-3clpV-RNAi strain infection group
SA206485clpv6-1clpV-RNAi strain infection group
SA206486clpv6-2clpV-RNAi strain infection group
SA206487clpv6-2-mclpV-RNAi strain infection group
SA206488clpv12-2clpV-RNAi strain infection group
SA206489clpv12-3clpV-RNAi strain infection group
SA206490clpv1d-2clpV-RNAi strain infection group
SA206491clpv1d-3clpV-RNAi strain infection group
SA206492clpv1d-4clpV-RNAi strain infection group
SA206493clpv1d-1clpV-RNAi strain infection group
SA206494clpv12-7clpV-RNAi strain infection group
SA206495clpv12-4clpV-RNAi strain infection group
SA206496clpv12-5clpV-RNAi strain infection group
SA206497clpv12-6clpV-RNAi strain infection group
SA206498clpv6-1-mclpV-RNAi strain infection group
SA206499clpv3d-5clpV-RNAi strain infection group
SA206500clpv1d-3-mclpV-RNAi strain infection group
SA206501clpv1d-2-mclpV-RNAi strain infection group
SA206502clpv4d-7clpV-RNAi strain infection group
SA206503clpv12-7-mclpV-RNAi strain infection group
SA206504clpv1d-4-mclpV-RNAi strain infection group
SA206505clpv1d-5-mclpV-RNAi strain infection group
SA206506clpv2d-1-mclpV-RNAi strain infection group
SA206507clpv1d-7-mclpV-RNAi strain infection group
SA206508clpv1d-6-mclpV-RNAi strain infection group
SA206509clpv12-6-mclpV-RNAi strain infection group
SA206510clpv12-5-mclpV-RNAi strain infection group
SA206511clpv6-6-mclpV-RNAi strain infection group
SA206512clpv6-5-mclpV-RNAi strain infection group
SA206513clpv6-4-mclpV-RNAi strain infection group
SA206514clpv6-3-mclpV-RNAi strain infection group
SA206515clpv6-7-mclpV-RNAi strain infection group
SA206516clpv12-1-mclpV-RNAi strain infection group
SA206517clpv12-4-mclpV-RNAi strain infection group
SA206518clpv12-3-mclpV-RNAi strain infection group
SA206519clpv12-2-mclpV-RNAi strain infection group
SA206520clpv2d-2-mclpV-RNAi strain infection group
SA206521clpv1d-1-mclpV-RNAi strain infection group
SA206522clpv4d-2-mclpV-RNAi strain infection group
SA206523clpv4d-1-mclpV-RNAi strain infection group
SA206524clpv3d-7-mclpV-RNAi strain infection group
SA206525clpv4d-3-mclpV-RNAi strain infection group
SA206526clpv4d-4-mclpV-RNAi strain infection group
SA206527clpv2d-3-mclpV-RNAi strain infection group
SA206528clpv4d-6-mclpV-RNAi strain infection group
SA206529clpv4d-5-mclpV-RNAi strain infection group
SA206530clpv3d-6-mclpV-RNAi strain infection group
SA206531clpv4d-7-mclpV-RNAi strain infection group
SA206532clpv2d-7-mclpV-RNAi strain infection group
SA206533clpv2d-6-mclpV-RNAi strain infection group
SA206534clpv2d-5-mclpV-RNAi strain infection group
SA206535clpv3d-5-mclpV-RNAi strain infection group
SA206536clpv3d-1-mclpV-RNAi strain infection group
SA206537clpv2d-4-mclpV-RNAi strain infection group
SA206538clpv3d-4-mclpV-RNAi strain infection group
SA206539clpv3d-2-mclpV-RNAi strain infection group
SA206540clpv3d-3-mclpV-RNAi strain infection group
SA206373PBS1d-2Control
SA206374PBS1d-1Control
SA206375PBS12-6Control
SA206376PBS1d-3Control
SA206377PBS12-7Control
SA206378PBS1d-4Control
SA206379PBS1d-7Control
SA206380PBS1d-6Control
SA206381PBS1d-5Control
SA206382PBS12-5Control
SA206383PBS12-3Control
SA206384PBS6-5Control
SA206385PBS6-4Control
SA206386PBS6-3Control
SA206387PBS6-2Control
SA206388PBS6-6Control
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Collection:

Collection ID:CO002233
Collection Summary:The spleens of E. coioides were collected at 6, 12, 24, 48, 72 and 96 hours post injection (hpi). After phenotypic observation of spleen tissue, grouper spleen samples were collected and accurately weighed (~15 mg) and stored in a -80 °C freezer.
Collection Protocol Comments:E.coioides.pdf
Sample Type:Spleen
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002252
Treatment Summary:E. coioides of the infection group were intrapleurally injected with 105 colony-forming units per fish (cfu/fish) of P. plecoglossicida (wild-type strain or clpV-RNAi strain), while control E. coioides received an equivalent volume of phosphate-buffered saline (PBS).

Sample Preparation:

Sampleprep ID:SP002246
Sampleprep Summary:The deep-frozen spleen tissue in each replicate was accurately weighed (about 15 mg) and then transferred to an Eppendorf tube. Each sample was first spiked with 300 μL of methanol containing internal standards and then homogenized at 65 Hz for 2.5 min. The homogenate was mixed with 1 mL of MTBE, and thoroughly vortexed for 30 min. Then, 300 μL of Milli-Q water was added to the tube, followed by vortexing for 1 min and centrifugation for 10 min to form a two-phase system (12,000 rpm, 4 ℃). Each specimen was prepared by mixing 250 μL of the top layer plus 150 μL of the bottom layer accurately and then vacuum-dried in a Speedvac concentrator (Thermo Scientific, USA).

Combined analysis:

Analysis ID AN003528 AN003529
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters Acquity BEH C8 (100 x 2.1mm, 1.7um) Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap Thermo Q Exactive HF-X Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH002606
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003286
Analysis ID:AN003528
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:-
Ion Mode:POSITIVE
  
MS ID:MS003287
Analysis ID:AN003529
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:-
Ion Mode:NEGATIVE
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