Summary of Study ST003835

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 PR002395. The data can be accessed directly via it's Project DOI: 10.21228/M8283D This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST003835
Study Titlemetabolomics of wild-type and TauT-/- leukemia cells
Study SummaryC57BL/6J mice conditioned with irradiation were transplanted with wild type and TauT-/- leukemia stem cells. The mice were sacrificed on days 11-13 post-transplant. Spleens from leukemic mice were quickly dissected and dissociated in Hanks’ balanced salt solution (Gibco) with 5% fetal bovine serum and 2mM EDTA at 4 degrees C. The leukemia cells were stained for Lin+ (CD3ε-, CD4-, CD8-, Gr1-, CD11b/Mac-1-, TER119-, CD45R/B220- and CD19-) markers and were magnetically depleted using LD columns (Milteny Biotec). Lin- leukemia stem cell fraction was washed with PBS containing 5mM glucose and centrifuged at 3000g for 1 min, snap frozen, and processed for untargeted metabolomics
Institute
University of Rochester Medical Center
Last NameSmith
First NameBradley
Address575 Elmwood Ave, Rochester, NY, 14620
Emailbradley_smith@urmc.rochester.edu
Phone585-275-1445
Submit Date2025-03-27
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-04-04
Release Version1
Bradley Smith Bradley Smith
https://dx.doi.org/10.21228/M8283D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002395
Project DOI:doi: 10.21228/M8283D
Project Title:Metabolomics of wild-type and TauT-/- leukemia cells.
Project Summary:We carried out untargeted metabolomic analysis of Lin- leukemia stem cells from mice bearing wild type and TauT-/- leukemias. Briefly, C57BL/6J mice were retro-orbitally transplanted with wild type and TauT-/- leukemia stem cells. The mice were sacrificed on days 11-13. Leukemia cells were isolated and magnetically enriched for lin- leukemia stem cells. Untargeted metabolomic analysis was carried out to identify metabolic changes induced by inhibiting taurine uptake in leukemia cells.
Institute:University of Rochester Medical Center
Last Name:Smith
First Name:Bradley
Address:575 Elmwood Ave, Rochester, NY, 14620
Email:bradley_smith@urmc.rochester.edu
Phone:585-275-1445

Subject:

Subject ID:SU003969
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

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

mb_sample_id local_sample_id Genotype
SA419413BcCML_KO_7_23BcCML_KO
SA419414BcCML_KO_2_18BcCML_KO
SA419415BcCML_KO_9_25BcCML_KO
SA419416BcCML_KO_8_24BcCML_KO
SA419417BcCML_KO_1_17BcCML_KO
SA419418BcCML_KO_6_22BcCML_KO
SA419419BcCML_KO_4_20BcCML_KO
SA419420BcCML_KO_3_19BcCML_KO
SA419421BcCML_KO_5_21BcCML_KO
SA419422BcCML_WT_10_10BcCML_WT
SA419423BcCML_WT_16_16BcCML_WT
SA419424BcCML_WT_15_15BcCML_WT
SA419425BcCML_WT_14_14BcCML_WT
SA419426BcCML_WT_13_13BcCML_WT
SA419427BcCML_WT_12_12BcCML_WT
SA419428BcCML_WT_11_11BcCML_WT
SA419429BcCML_WT_8_8BcCML_WT
SA419430BcCML_WT_9_9BcCML_WT
SA419431BcCML_WT_7_7BcCML_WT
SA419432BcCML_WT_6_6BcCML_WT
SA419433BcCML_WT_4_4BcCML_WT
SA419434BcCML_WT_3_3BcCML_WT
SA419435BcCML_WT_2_2BcCML_WT
SA419436BcCML_WT_1_1BcCML_WT
SA419437BcCML_WT_5_5BcCML_WT
Showing results 1 to 25 of 25

Collection:

Collection ID:CO003962
Collection Summary:C57BL/6J mice conditioned with irradiation were transplanted with wild type and TauT-/- leukemia stem cells. The mice were sacrificed on days 11-13 post-transplant. Spleens from leukemic mice were quickly dissected and dissociated in Hanks’ balanced salt solution (Gibco) with 5% fetal bovine serum and 2mM EDTA at 4°C. The leukemia cells were stained for Lin+ (CD3ε-, CD4-, CD8-, Gr1-, CD11b/Mac-1-, TER119-, CD45R/B220- and CD19-) markers and were magnetically depleted using LD columns (Milteny Biotec). Lin- leukemia stem cell fraction was washed with PBS containing 5 mM glucose and centrifuged at 3000g for 1 min and snap frozen.
Sample Type:Leukemia cells

Treatment:

Treatment ID:TR003978
Treatment Summary:Not applicable

Sample Preparation:

Sampleprep ID:SP003975
Sampleprep Summary:Frozen cell pellets were resuspended at 2 million cells per 1 mL of 80% MeOH via vortexing, transferred to -80°C for 30 min and then regular ice for 30 minutes with vortexing every 10 minutes. Next, samples were centrifuged at 17,000x g for 10 minutes and 90% of supernatant was dried down in a vacuum evaporator (Thermo). Samples were reconstituted in 50% acetonitrile (A955, Fisher Scientific), at a volume equal to 10% of dried down volume, and transferred to glass vials for LC/MS analysis.

Combined analysis:

Analysis ID AN006297 AN006298
Chromatography ID CH004779 CH004780
MS ID MS005999 MS006000
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters XBridge XP BEH Amide (150 mm x 2.1 mm, 2.5 µm) Waters XBridge XP BEH Amide (150 mm x 2.1 mm, 2.5 µm)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Orbitrap Exploris 240 Thermo Orbitrap Exploris 240
Ion Mode NEGATIVE POSITIVE
Units area area

Chromatography:

Chromatography ID:CH004779
Instrument Name:Thermo Vanquish
Column Name:Waters XBridge XP BEH Amide (150 mm x 2.1 mm, 2.5 µm)
Column Temperature:25°C
Flow Gradient:0 minutes, 100% B; 2 minutes, 100% B; 3 minutes, 90% B; 5 minutes, 90% B; 6 minutes, 85% B; 7 minutes, 85% B; 8 minutes, 75% B; 9 minutes, 75% B; 10 minutes, 55% B; 12 minutes, 55% B; 13 minutes, 35%, 20 minutes, 35% B; 20.1 minutes, 35% B; 20.6 minutes, 100% B; 22.2 minutes, 100% B
Flow Rate:150 μL/min for first 22.7 minutes, then 150 μL/min for 22.7 to 28 minutes
Solvent A:100% water; 10 mM ammonium acetate; 0.1% ammonium hydroxide; 0.1% medronic acid
Solvent B:90% acetonitrile/10% water; 10 mM ammonium acetate; 0.1% ammonium hydroxide; 0.1% medronic acid
Chromatography Type:HILIC
  
Chromatography ID:CH004780
Instrument Name:Thermo Vanquish
Column Name:Waters XBridge XP BEH Amide (150 mm x 2.1 mm, 2.5 µm)
Column Temperature:25°C
Flow Gradient:0 minutes, 100% B; 2 minutes, 100% B; 3 minutes, 90% B; 5 minutes, 90% B; 6 minutes, 85% B; 7 minutes, 85% B; 8 minutes, 75% B; 9 minutes, 75% B; 10 minutes, 55% B; 12 minutes, 55% B; 13 minutes, 35%, 20 minutes, 35% B; 20.1 minutes, 35% B; 20.6 minutes, 100% B; 22.2 minutes, 100% B
Flow Rate:150 μL/min for first 22.7 minutes, then 150 μL/min for 22.7 to 28 minutes
Solvent A:100% water; 10 mM ammonium formate; 0.125% formic acid
Solvent B:90% acetonitrile/10% water; 10 mM ammonium formate; 0.125% formic acid
Chromatography Type:HILIC

MS:

MS ID:MS005999
Analysis ID:AN006297
Instrument Name:Thermo Orbitrap Exploris 240
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The H-ESI source was operated in negative mode at spray voltage 2500 with the following parameters: sheath gas 35 au, aux gas 7 au, sweep gas 0 au, ion transfer tube temperature 320°C, vaporizer temperature 275°C, mass range 70 to 1000 m/z, full scan MS1 mass resolution of 120,000 FWHM, RF lens at 70%, and standard automatic gain control (AGC). Data acquisition software: Thermo XCalibur Data processing and feature assignment software: Thermo Compound Discoverer
Ion Mode:NEGATIVE
  
MS ID:MS006000
Analysis ID:AN006298
Instrument Name:Thermo Orbitrap Exploris 240
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The H-ESI source was operated in positive mode at spray voltage 3500 with the following parameters: sheath gas 35 au, aux gas 7 au, sweep gas 0 au, ion transfer tube temperature 320°C, vaporizer temperature 275°C, mass range 70 to 1000 m/z, full scan MS1 mass resolution of 120,000 FWHM, RF lens at 70%, and standard automatic gain control (AGC). Data acquisition software: Thermo XCalibur Data processing and feature assignment software: Thermo Compound Discoverer
Ion Mode:POSITIVE
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