Summary of Study ST000307

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 PR000247. The data can be accessed directly via it's Project DOI: 10.21228/M8VG6R This work is supported by NIH grant, U2C- DK119886.

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Study IDST000307
Study TitleTargeting CRBN to alter CD8 T cell metabolism
Study TypeT cell activation
Study SummaryThe purpose of this study was to evaluate the metabolic profile of different treatments of T-Cells among two separate mouse genotypes.
Institute
University of Florida
DepartmentSECIM
LaboratoryMoffitt Cancer Center - Immunology
Last NameSwearingen
First NameRebecca
Address-
Emailrebecca.swearingen@moffitt.org
Phone-
Submit Date2015-12-22
Num Groups12
Total Subjects60
Raw Data AvailableYes
Raw Data File Type(s)mzXML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2016-12-22
Release Version1
Rebecca Swearingen Rebecca Swearingen
https://dx.doi.org/10.21228/M8VG6R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000247
Project DOI:doi: 10.21228/M8VG6R
Project Title:CRBN's role in T cell activation
Project Summary:Targeting CRBN to alter CD8 T cell metabolism
Institute:Moffitt Cancer Center
Department:Immunology
Last Name:Burnette
First Name:Pearlie
Address:-
Email:pearlie.burnette@moffitt.org
Phone:-

Subject:

Subject ID:SU000327
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Animal Animal Supplier:WT (CRBN +/+) mice are from Jackson labs and CRBN -/- mice have been bred at Moffitt Cancer Center
Animal Housing:Standard bedding + cotton pads, hepa filtered air
Animal Light Cycle:Dark 6pm-6am
Animal Feed:Feed from Harlan, not sterile
Animal Water:autoclaved H2O
Animal Inclusion Criteria:Animals used in this experiment were sex-matched and age matched. The ages were 8-12 weeks old in both sets of experiments
Species Group:Mammal

Factors:

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

mb_sample_id local_sample_id Strain Treatment
SA013957CD3 + CD28 WT1 042215CRBN +/+ anti-CD3 & anti-CD28 stimulation
SA013958CD3 + CD28 WT3CRBN +/+ anti-CD3 & anti-CD28 stimulation
SA013959CD3 + CD28 WT4CRBN +/+ anti-CD3 & anti-CD28 stimulation
SA013960CD3 + CD28 WT3 042215CRBN +/+ anti-CD3 & anti-CD28 stimulation
SA013961CD3 + CD28 WT5 042215CRBN +/+ anti-CD3 & anti-CD28 stimulation
SA013962CD3 + CD28 WT1CRBN +/+ anti-CD3 & anti-CD28 stimulation
SA013963CD3 + CD28 WT2CRBN +/+ anti-CD3 & anti-CD28 stimulation
SA013964CD3 + CD28 WT5CRBN +/+ anti-CD3 & anti-CD28 stimulation
SA013965CD3 + CD28 WT4 042215CRBN +/+ anti-CD3 & anti-CD28 stimulation
SA013966CD3 + CD28 WT2 042215CRBN +/+ anti-CD3 & anti-CD28 stimulation
SA013987CD3 + CD28 KO5CRBN -/- anti-CD3 & anti-CD28 stimulation
SA013988CD3 + CD28 KO4CRBN -/- anti-CD3 & anti-CD28 stimulation
SA013989CD3 + CD28 KO1CRBN -/- anti-CD3 & anti-CD28 stimulation
SA013990CD3 + CD28 KO5 042215CRBN -/- anti-CD3 & anti-CD28 stimulation
SA013991CD3 + CD28 KO3 042215CRBN -/- anti-CD3 & anti-CD28 stimulation
SA013992CD3 + CD28 KO2CRBN -/- anti-CD3 & anti-CD28 stimulation
SA013993CD3 + CD28 KO1 042215CRBN -/- anti-CD3 & anti-CD28 stimulation
SA013994CD3 + CD28 KO3CRBN -/- anti-CD3 & anti-CD28 stimulation
SA013995CD3 + CD28 KO2 042215CRBN -/- anti-CD3 & anti-CD28 stimulation
SA013996CD3 + CD28 KO4 042215CRBN -/- anti-CD3 & anti-CD28 stimulation
SA013967CD3 WT1CRBN +/+ anti-CD3 stimulation
SA013968CD3 WT3 042215CRBN +/+ anti-CD3 stimulation
SA013969CD3 WT4 042215CRBN +/+ anti-CD3 stimulation
SA013970CD3 WT5 042215CRBN +/+ anti-CD3 stimulation
SA013971CD3 WT1 042215CRBN +/+ anti-CD3 stimulation
SA013972CD3 WT2 042215CRBN +/+ anti-CD3 stimulation
SA013973CD3 WT4CRBN +/+ anti-CD3 stimulation
SA013974CD3 WT3CRBN +/+ anti-CD3 stimulation
SA013975CD3 WT5CRBN +/+ anti-CD3 stimulation
SA013976CD3 WT2CRBN +/+ anti-CD3 stimulation
SA013997CD3 KO1CRBN -/- anti-CD3 stimulation
SA013998CD3 KO2 042215CRBN -/- anti-CD3 stimulation
SA013999CD3 KO3 042215CRBN -/- anti-CD3 stimulation
SA014000CD3 KO4 042215CRBN -/- anti-CD3 stimulation
SA014001CD3 KO2CRBN -/- anti-CD3 stimulation
SA014002CD3 KO3CRBN -/- anti-CD3 stimulation
SA014003CD3 KO5 042215CRBN -/- anti-CD3 stimulation
SA014004CD3 KO4CRBN -/- anti-CD3 stimulation
SA014005CD3 KO1 042215CRBN -/- anti-CD3 stimulation
SA014006CD3 KO5CRBN -/- anti-CD3 stimulation
SA013977Naive WT 4 042215CRBN +/+ unstimulated
SA013978Naive WT 5 042215CRBN +/+ unstimulated
SA013979Naive WT 4CRBN +/+ unstimulated
SA013980Naive WT 5CRBN +/+ unstimulated
SA013981Naive WT 3 042215CRBN +/+ unstimulated
SA013982Naive WT 2 042215CRBN +/+ unstimulated
SA013983Naive WT 3CRBN +/+ unstimulated
SA013984Naive WT 2CRBN +/+ unstimulated
SA013985Naive WT 1CRBN +/+ unstimulated
SA013986Naive WT 1 042215CRBN +/+ unstimulated
SA014007Naive KO5 042215CRBN -/- unstimulated
SA014008Naive KO3CRBN -/- unstimulated
SA014009Naive KO2CRBN -/- unstimulated
SA014010Naive KO1CRBN -/- unstimulated
SA014011Naive KO4CRBN -/- unstimulated
SA014012Naive KO5CRBN -/- unstimulated
SA014013Naive KO2 042215CRBN -/- unstimulated
SA014014Naive KO3 042215CRBN -/- unstimulated
SA014015Naive KO4 042215CRBN -/- unstimulated
SA014016Naive KO1 042215CRBN -/- unstimulated
Showing results 1 to 60 of 60

Collection:

Collection ID:CO000321
Collection Summary:-
Sample Type:cell
Collection Method:centrifuged in ficoll-gradient to remove debris, then washed in PBS
Collection Time:0 or 24 hours after stimulation
Storage Conditions:-80°C
Collection Vials:15mL conical tubes
Storage Vials:microfuge tubes

Treatment:

Treatment ID:TR000341
Treatment Summary:-
Animal Anesthesia:CO2 asphyxiation
Animal Acclimation Duration:Mice from Jackson are subjected to a week-long acclimation period in our facility prior to experimental use.
Animal Endp Tissue Coll List:Spleen into cell culture media
Cell Growth Container:96-well round-bottom plate that was coated with anti-CD3 antibody
Cell Growth Rate:Murine T cells generally divide after 48-72 hours of stimulation.
Cell Media:RPMI 1640 with 10% FBS, pen/strep, gentamycin, NEAA, Sodium pyruvate, fungizone (Amphotericin B), 2-mercaptoethanol
Cell Envir Cond:37°C, normoxic conditions

Sample Preparation:

Sampleprep ID:SP000335
Sampleprep Summary:-
Sampleprep Protocol Filename:Consolidated Cellular Metabolomics with DNA quant.pdf
Sample Spiking:Appendix A - Internal Standard Prep GLCMS.pdf

Combined analysis:

Analysis ID AN000486 AN000487
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Scientific-Dionex Ultimate 3000 Thermo Scientific-Dionex Ultimate 3000
Column ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
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 Peak area Peak area

Chromatography:

Chromatography ID:CH000347
Methods Filename:Metabolomics_LCMSProtocol.pdf
Instrument Name:Thermo Scientific-Dionex Ultimate 3000
Column Name:ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
Flow Rate:0.350mL/min-0.600mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS000424
Analysis ID:AN000486
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
Analysis Protocol File:Metabolomics_LCMSProtocol.pdf
  
MS ID:MS000425
Analysis ID:AN000487
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
Analysis Protocol File:Metabolomics_LCMSProtocol.pdf
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