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

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 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.

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

Analysis:

Analysis ID:AN006297
Analysis Type:MS
Chromatography ID:CH004779
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003835_AN006297_Results.txt
Units:area
  
Analysis ID:AN006298
Analysis Type:MS
Chromatography ID:CH004780
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003835_AN006298_Results.txt
Units:area
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