Summary of Study ST000460

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 IDST000460
Study TitleEffect of ATG7 reconstitution in AGY571 cells
Study TypeCells are treated with vehicle or Doxycycline - to induce expression of GFP or ATG7
Study SummaryAGY571 cells engineered to express Dox-inducible GFP or ATG7 were treated with 500 ng/mL or 1 ug/mL Doxycycline for 48 hours. Assessing the effects of ATG7 reexpression in B cell lymphoma.
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 Groups5
Total Subjects15
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:SU000481
Subject Type:Cells
Subject Species:Mus musculus
Taxonomy ID:10090
Cell Strain Details:AGY571
Subject Comments:See study design section for cell number per sample for cell counts
Cell Primary Immortalized:Immortalized
Species Group:Mammal

Factors:

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

mb_sample_id local_sample_id Treatment Dox Concentration Ectopic Gene Expression
SA023241AGY571_009Doxycycline 1 ug/mL ATG7
SA023242AGY571_007Doxycycline 1 ug/mL ATG7
SA023243AGY571_008Doxycycline 1 ug/mL ATG7
SA023244AGY571_003Doxycycline 1 ug/mL GFP (ATG7-/-)
SA023245AGY571_001Doxycycline 1 ug/mL GFP (ATG7-/-)
SA023246AGY571_002Doxycycline 1 ug/mL GFP (ATG7-/-)
SA023247AGY571_013Doxycycline 500 ng/mL ATG7
SA023248AGY571_014Doxycycline 500 ng/mL ATG7
SA023249AGY571_015Doxycycline 500 ng/mL ATG7
SA023250AGY571_012Doxycycline 500 ng/mL GFP (ATG7-/-)
SA023251AGY571_010Doxycycline 500 ng/mL GFP (ATG7-/-)
SA023252AGY571_011Doxycycline 500 ng/mL GFP (ATG7-/-)
SA023253AGY571_006Vehicle 0 ug/mL None (ATG7-/- backgound)
SA023254AGY571_005Vehicle 0 ug/mL None (ATG7-/- backgound)
SA023255AGY571_004Vehicle 0 ug/mL None (ATG7-/- backgound)
Showing results 1 to 15 of 15

Collection:

Collection ID:CO000475
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:48 hours after Dox treatment
Storage Conditions:Pellet at -80C
Storage Vials:1.5 mL microfuge tube
Tissue Cell Identification:AGY571 cells

Treatment:

Treatment ID:TR000495
Treatment Summary:Cells were treated with vehicle (dH2O) or 500 ng/mL doxycycline.
Treatment Compound:Doxycycline
Treatment Dose:0.5-1.0 ug/mL
Treatment Dosevolume:5 mL
Treatment Doseduration:48 hours
Treatment Vehicle:dH2O
Cell Growth Container:6-well plate

Sample Preparation:

Sampleprep ID:SP000488
Sampleprep Summary:Amino acid
Sampleprep Protocol Filename:SB_AA_Assay.pdf

Combined analysis:

Analysis ID AN000721
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:CH000518
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:MS000641
Analysis ID:AN000721
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Amino Acids
Ion Mode:POSITIVE
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