Summary of Study ST001211

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 PR000814. The data can be accessed directly via it's Project DOI: 10.21228/M8G40M 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 IDST001211
Study TitleMetabolomic Markers of Methotrexate Response, In Vitro
Study SummaryErythroblastoid cells (K562) maintained in logarithmic growth phase were treated with 1000 nM methotrexate or vehicle alone (i.e. D-PBS) under standard culture conditions for 24 hours. Cellular response to methotrexate was measured based on anti-proliferative activity by cell counting. Cells were washed, flash frozen in liquid nitrogen and submitted for metabolomics analysis to the NIH West Coast Metabolomics Center.
Institute
University of Kansas
DepartmentPharmacy Practice
LaboratoryFunk Lab
Last NameFunk
First NameRyan
Address2106 Olathe Boulevard
Emailryanfunk@kumc.edu
Phone9135885000
Submit Date2019-07-03
Num Groups2
Total Subjects20 samples
Analysis Type DetailGC-MS/LC-MS
Release Date2020-01-06
Release Version1
Ryan Funk Ryan Funk
https://dx.doi.org/10.21228/M8G40M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000814
Project DOI:doi: 10.21228/M8G40M
Project Title:Metabolic Markers of Methotrexate Response
Project Type:In Vitro
Project Summary:Untargeted metabolomics study of methotrexate pharmacological response.
Institute:University of Kansas
Department:Pharmacy Practice
Laboratory:Funk
Last Name:Funk
First Name:Ryan
Address:2106 Olathe Boulevard, Kansas City, Kansas, 66160, USA
Email:ryanfunk@kumc.edu
Phone:9139456904
Funding Source:KL2TR002367

Subject:

Subject ID:SU001278
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:53 years
Gender:Female
Cell Biosource Or Supplier:Coriell
Cell Strain Details:GM05372
Cell Primary Immortalized:Epstein-Barr Virus
Cell Passage Number:Six
Cell Counts:15 million

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Group
SA0852109Control
SA08521110Control
SA0852121Control
SA0852137Control
SA0852148Control
SA0852156Control
SA0852162Control
SA0852174Control
SA0852183Control
SA0852195Control
SA08522018Methotrexate
SA08522119Methotrexate
SA08522220Methotrexate
SA08522317Methotrexate
SA08522411Methotrexate
SA08522512Methotrexate
SA08522613Methotrexate
SA08522714Methotrexate
SA08522815Methotrexate
SA08522916Methotrexate
Showing results 1 to 20 of 20

Collection:

Collection ID:CO001272
Collection Summary:Cells were counted, a volume containing 15 million cells were collected, washed with
Sample Type:K562
Storage Conditions:-80℃
Tissue Cell Quantity Taken:15 million cells

Treatment:

Treatment ID:TR001293
Treatment Summary:Cells were maintained under normal growth conditions in a humidified, temperature- and CO2-controlled incubator at 37ºC and 5% CO2. Cells were kept at density between 2.0x105 and 1.0x106 cells/mL to maintain logarithmic growth conditions to promote maximum proliferative activity over the experimental period. All experiments were conducted within six passages following removal from cryopreservation. On the day of experimentation, K562 cells were seeded at a density of 4.0x105 cells/mL and exposed to 1000 nM MTX or D-PBS (i.e. vehicle) for 24 hours under normal growth conditions.
Treatment Compound:Methotrexate
Treatment Route:In Media
Treatment Dose:1000 nM
Treatment Doseduration:24 hours
Treatment Vehicle:Dulbecco's Phosphate Buffered Saline (without Calcium/Magnesium)
Cell Storage:Liquid Nitrogen
Cell Growth Container:T-175 Flask
Cell Growth Config:Suspension
Cell Inoc Proc:Seeded at 4.010^5 cells/mL
Cell Media:RPMI 1640 medium (catalog no. 61870-127, ThermoFisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (catalog no. S11150, Atlanta Biologicals, Lawrenceville, GA) along with 100 units/mL penicillin and 1,000 units/mL streptomycin (catalog no. 15140122, ThermoFisher Scientific, Waltham, MA)
Cell Envir Cond:humidified, temperature- and CO2-controlled incubator at 37ºC and 5% CO2
Cell Harvesting:Counted and a volume containing 15x10^6 cells were collected, washed, flash frozen in liquid nitrogen
Cell Pct Confluence:NA
Cell Media Lastchanged:24 hours prior to collection

Sample Preparation:

Sampleprep ID:SP001286
Sampleprep Summary:Cell pellets were sent to the West Coast Metabolomics Center and were processed on laboratory Standard Operating Procedures for Sample Preparation of Blood Plasma or Serum Samples for Lipidomic, Biogenic Amine, and Primary Metabolomic Analysis using a biphasic MeOH/MTBE/Water extraction procedure. The upper organic phase was used for lipidomics analysis and the aqueous phase was used for analysis of primary metabolism and biogenic amines.

Combined analysis:

Analysis ID AN002016 AN002017 AN002018 AN002019
Analysis type MS MS MS MS
Chromatography type GC HILIC Reversed phase Reversed phase
Chromatography system Leco Pegasus IV GC Agilent 6530 Agilent 6530 Agilent 6530
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
MS Type EI ESI ESI ESI
MS instrument type GC-TOF QTOF QTOF QTOF
MS instrument name Leco Pegasus IV TOF Agilent 6530 QTOF Agilent 6530 QTOF Agilent 6550 QTOF
Ion Mode NEGATIVE POSITIVE POSITIVE NEGATIVE
Units Peak height Peak height Peak height Peak height

Chromatography:

Chromatography ID:CH001458
Chromatography Summary:Primary Metabolism
Instrument Name:Leco Pegasus IV GC
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:GC
  
Chromatography ID:CH001459
Chromatography Summary:Biogenic Amines
Instrument Name:Agilent 6530
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Chromatography Type:HILIC
  
Chromatography ID:CH001460
Chromatography Summary:Lipidomics
Instrument Name:Agilent 6530
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:65
Flow Rate:0.6 mL/min
Solvent A:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:Reversed phase

MS:

MS ID:MS001869
Analysis ID:AN002016
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols.
Ion Mode:NEGATIVE
Analysis Protocol File:Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf
  
MS ID:MS001870
Analysis ID:AN002017
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols.
Ion Mode:POSITIVE
Analysis Protocol File:Data_Dictionary_Fiehn_laboratory_HILIC_QTOF_MS.pdf
  
MS ID:MS001871
Analysis ID:AN002018
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols.
Ion Mode:POSITIVE
Analysis Protocol File:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf
  
MS ID:MS001872
Analysis ID:AN002019
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols.
Ion Mode:NEGATIVE
Analysis Protocol File:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf
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