Summary of Study ST000459

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 PR000354. The data can be accessed directly via it's Project DOI: 10.21228/M8930Q This work is supported by NIH grant, U2C- DK119886.

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Study IDST000459
Study TitleEffect of Odc knockout on amino acid steady state levels of Eμ-Myc lymphomas
Study TypeCells are treated with vehicle or Doxycycline - to promote deletion of Odc gene
Study SummaryCells were collected 48 hours after treatment with Dox.
Institute
University of Florida
DepartmentSECIM
LaboratoryJohn Cleveland
Last NameFernandez
First NameMario
Address12902 Magnolia Drive, MRC 4-West
Emailmario.fernandez@moffitt.org
Phone813-745-5140
Submit Date2016-09-08
Num Groups4
Total Subjects12
Study CommentsGroups collected in triplicate per time point, either treated or untreated with Doxycycline.
Analysis Type DetailLC-MS
Release Date2020-07-08
Release Version1
Mario Fernandez Mario Fernandez
https://dx.doi.org/10.21228/M8930Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000354
Project DOI:doi: 10.21228/M8930Q
Project Title:The effect of BCAT1 knockdown on amino acid homeostasis
Project Type:Amino acid steady-state level analysis
Project Summary:Raji cells, a Burkitt lymphoma, expressing a Dox-inducible short hairpin targeting BCAT1 were collected in triplicate at 0, 48, 96, and 144 hours.
Institute:H. Lee Moffitt Cancer Center
Department:Tumor Biology
Laboratory:John Cleveland
Last Name:Fernandez
First Name:Mario
Address:12902 Magnolia Drive, MRC 4-West
Email:mario.fernandez@moffitt.org
Phone:813-745-5140
Funding Source:5R01CA154739

Subject:

Subject ID:SU000480
Subject Type:Cells
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:Eμ-Myc;rtTA;Odc fl/fl - C57BL/6
Cell Strain Details:YA95
Cell Primary Immortalized:Immortalized
Cell Passage Number:5
Cell Counts:6e6 to 20e6/sample
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Treatment Genotype
SA023229YA95_11Doxycycline Odc -/-
SA023230YA95_10Doxycycline Odc -/-
SA023231YA95_12Doxycycline Odc -/-
SA023232YA95_6Doxycycline Odc WT
SA023233YA95_4Doxycycline Odc WT
SA023234YA95_5Doxycycline Odc WT
SA023235YA95_9Vehicle Odc WT
SA023236YA95_7Vehicle Odc WT
SA023237YA95_2Vehicle Odc WT
SA023238YA95_3Vehicle Odc WT
SA023239YA95_1Vehicle Odc WT
SA023240YA95_8Vehicle Odc WT
Showing results 1 to 12 of 12

Collection:

Collection ID:CO000474
Collection Summary:Cells were counted, cells were collected via centrifugation, washed twice with cold 1x PBS, PBS removed and flash frozen. Pellets were saved at -80 C.
Sample Type:Cell
Collection Method:Pellet
Collection Location:Lab
Collection Frequency:Once at 48 hours post-treatment
Volumeoramount Collected:Depends on sample. Collected as many cells as available. Total cell number range between samples is 6e6 to 20e6 cells per pellet
Storage Conditions:Pellet
Storage Vials:1.5 mL microfuge tube
Tissue Cell Identification:YA95

Treatment:

Treatment ID:TR000494
Treatment Summary:Cells were treated with vehicle (dH2O) or 500 ng/mL doxycycline.
Treatment Compound:Doxycycline
Treatment Dose:500 ng/mL
Treatment Dosevolume:4 mL
Treatment Doseduration:48 hours
Treatment Vehicle:dH2O
Cell Growth Container:6-well plate

Sample Preparation:

Sampleprep ID:SP000487
Sampleprep Summary:Amino acid
Sampleprep Protocol Filename:SB_AA_Assay.pdf

Combined analysis:

Analysis ID AN000720
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1290 Infinity
Column Waters AccQ Tag (100 x 2mm,1.7um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name Agilent 6490 QQQ
Ion Mode POSITIVE
Units nmol/mg protein

Chromatography:

Chromatography ID:CH000517
Chromatography Summary:Amino Acid
Methods Filename:SB_AA_Assay.pdf
Instrument Name:Agilent 1290 Infinity
Column Name:Waters AccQ Tag (100 x 2mm,1.7um)
Column Temperature:55
Flow Rate:0.7 mL/min
Solvent A:AccQ·Tag Eluent A
Solvent B:accQ·Tag Eluent B
Chromatography Type:Reversed phase

MS:

MS ID:MS000640
Analysis ID:AN000720
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
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