Summary of Study ST001897

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 PR001193. The data can be accessed directly via it's Project DOI: 10.21228/M8H419 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 IDST001897
Study TitleA local source of insulin in the eye governed by phagocytosis and starvation
Study TypeUntargeted Metabolomics
Study SummaryUntargeted metabolite analysis was performed on a Thermo Orbitrap IDX Tribrid MS to understand changes in metabolites in eye retina and RPE tissue during starvation. This study also probes the role of certain metabolites during phagocytosis.
Institute
University of Virginia
DepartmentCenter of Cell Clearance , Microbiology, Immunology, and Cancer Biology
LaboratoryKodi Ravichandraan Lab
Last NameEtchegaray
First NameIker
AddressCenter of Cell Clearance , Microbiology, Immunology, and Cancer Biology
Emailkr4h@virginia.edu; jie3c@virginia.edu; nw5es@virginia.edu;
Phone4023109931
Submit Date2021-08-02
Num Groups4
Total Subjects2
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-12-05
Release Version1
Iker Etchegaray Iker Etchegaray
https://dx.doi.org/10.21228/M8H419
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001193
Project DOI:doi: 10.21228/M8H419
Project Title:Untargeted metabolomics to understand metabolism of local source of insulin in the eye governed by phagocytosis and starvation
Project Type:Untargeted Metabolomics (UPLC-MS/MS)
Project Summary:Untargeted metabolite analysis was performed on a Thermo Orbitrap IDX Tribrid MS to understand changes in metabolites in eye retina and RPE tissue during starvation. This study also probes the role of certain metabolites during phagocytosis.
Institute:University of Virginia
Department:Center of Cell Clearance , Microbiology, Immunology, and Cancer Biology
Laboratory:Kodi Ravichandraan Lab
Last Name:Etchegaray
First Name:Iker
Address:Department of Microbiology, Immunology, and Cancer Biology, University of Virginia
Email:jie3c@virginia.edu; kr4h@virginia.edu; nw5es@virginia.edu
Phone:4023109931

Subject:

Subject ID:SU001975
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammals

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id group
SA176068Sample_p_007KO_Retina
SA176069Sample_n_019KO_Retina
SA176070Sample_n_003KO_Retina
SA176071Sample_p_003KO_Retina
SA176072Sample_p_015KO_Retina
SA176073Sample_n_011KO_Retina
SA176074Sample_p_019KO_Retina
SA176075Sample_p_011KO_Retina
SA176076Sample_n_015KO_Retina
SA176077Sample_n_007KO_Retina
SA176058Sample_n_016KO_RPE
SA176059Sample_p_020KO_RPE
SA176060Sample_p_008KO_RPE
SA176061Sample_p_004KO_RPE
SA176062Sample_n_020KO_RPE
SA176063Sample_p_012KO_RPE
SA176064Sample_n_012KO_RPE
SA176065Sample_n_004KO_RPE
SA176066Sample_p_016KO_RPE
SA176067Sample_n_008KO_RPE
SA176078Sample_p_QC2QC
SA176079Sample_n_QC5QC
SA176080Sample_p_QC1QC
SA176081Sample_n_QC1QC
SA176082Sample_p_QC4QC
SA176083Sample_p_QC5QC
SA176084Sample_n_QC4QC
SA176085Sample_p_QC3QC
SA176086Sample_n_QC3QC
SA176087Sample_n_QC2QC
SA176098Sample_p_001WT_Retina
SA176099Sample_n_013WT_Retina
SA176100Sample_n_009WT_Retina
SA176101Sample_n_005WT_Retina
SA176102Sample_n_017WT_Retina
SA176103Sample_n_001WT_Retina
SA176104Sample_p_013WT_Retina
SA176105Sample_p_009WT_Retina
SA176106Sample_p_005WT_Retina
SA176107Sample_p_017WT_Retina
SA176088Sample_n_002WT_RPE
SA176089Sample_p_002WT_RPE
SA176090Sample_p_014WT_RPE
SA176091Sample_n_010WT_RPE
SA176092Sample_n_006WT_RPE
SA176093Sample_p_010WT_RPE
SA176094Sample_p_006WT_RPE
SA176095Sample_n_018WT_RPE
SA176096Sample_n_014WT_RPE
SA176097Sample_p_018WT_RPE
Showing results 1 to 50 of 50

Collection:

Collection ID:CO001968
Collection Summary:Overnight fasted mice were euthanized with avertin after light onset. Five replicates each of both Retinal and RPE tissues (from wild type and knock out mice) were harvested/dissected, flash frozen and stored in -80 ºC until extraction. Tissues were thawed on ice and extracted using methanol:chloroform (2:1) at 4C and phase separated using water. Top aq. phase was recovered as metabolite mixture and dried overnight in speedVac and reconstituted in 100 µL of 0.1% Formic acid in water. Ten µl from each tube was removed to create a pooled QC sample that was injected at the beginning and end of the MS sequence run and additional QC samples were injected after every 5 sample injection.
Sample Type:Eye tissue

Treatment:

Treatment ID:TR001987
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP001981
Sampleprep Summary:Overnight fasted mice were euthanized with avertin after light onset. Five replicates each of both Retinal and RPE tissues (from wild type and knock out mice) were harvested/dissected, flash frozen and stored in -80 ºC until extraction. Tissues were thawed on ice and extracted using methanol:chloroform (2:1) at 4C and phase separated using water. Top aq. phase was recovered as metabolite mixture and dried overnight in speedVac and reconstituted in 100 µL of 0.1% Formic acid in water. Ten µl from each tube was removed to create a pooled QC sample that was injected at the beginning and end of the MS sequence run and additional QC samples were injected after every 5 sample injection.
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Chromatography:

Chromatography ID:CH002276
Chromatography Summary:Low pH polar
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Temperature:30C
Flow Gradient:0-8 minutes 50% B, 8 – 13 minutes held at 98% B, 13.1 to 15.0 minutes revert to 0% B to re-equilibration for next injection
Flow Rate:0.25 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% methanol; 0.1% formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN003078
Analysis Type:MS
Chromatography ID:CH002276
Num Factors:5
Num Metabolites:284
Rt Units:Minutes
Units:intensity
  
Analysis ID:AN003079
Analysis Type:MS
Chromatography ID:CH002276
Num Factors:5
Num Metabolites:45
Rt Units:Minutes
Units:intensity
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