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MB Sample ID: SA085219

Local Sample ID:5
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

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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:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
5SA085219FL012829ControlGroup

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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