Summary of Study ST000458

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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 IDST000458
Study TitleEffect of BCAT1 knockdown on amino acid steady state levels of Raji cells
Study TypeCells are treated with vehicle or Doxycycline - to induce expression of BCAT1 short hairpin RNA.
Study SummaryCells were collected at 0, 48, 96 and 144 hours after Doxycycline addition
University of Florida
LaboratoryJohn Cleveland
Last NameFernandez
First NameMario
Address12902 Magnolia Drive, MRC 4-West
Submit Date2016-09-08
Num Groups7
Total Subjects21
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 application/zip

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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
Funding Source:5R01CA154739


Subject ID:SU000479
Subject Type:Cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Strain Details:Raji
Cell Primary Immortalized:Immortalized
Cell Passage Number:16
Cell Counts:2e6 to 5e6/sample
Species Group:Human


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

mb_sample_id local_sample_id Time Treatment
SA023211Raji_019144(hrs) Doxycycline
SA023212Raji_021144(hrs) Doxycycline
SA023213Raji_020144(hrs) Doxycycline
SA023214Raji_018144(hrs) Vehicle
SA023215Raji_017144(hrs) Vehicle
SA023216Raji_016144(hrs) Vehicle
SA023217Raji_00848(hrs) Doxycycline
SA023218Raji_00748(hrs) Doxycycline
SA023219Raji_00948(hrs) Doxycycline
SA023220Raji_00548(hrs) Vehicle
SA023221Raji_00648(hrs) Vehicle
SA023222Raji_00448(hrs) Vehicle
SA023223Raji_01396(hrs) Doxycycline
SA023224Raji_01496(hrs) Doxycycline
SA023225Raji_01596(hrs) Doxycycline
SA023226Raji_01196(hrs) Vehicle
SA023227Raji_01096(hrs) Vehicle
SA023228Raji_01296(hrs) Vehicle
SA023208Raji_002- Vehicle
SA023209Raji_003- Vehicle
SA023210Raji_001- Vehicle
Showing results 1 to 21 of 21


Collection ID:CO000473
Collection Summary:Cells were counted, 2e6 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:Every 48 hours, up to 144 hours
Volumeoramount Collected:2e6 cells for 0, 48 and 144 time point. 5e6 cells for 96 hour time point
Storage Conditions:Pellet
Storage Vials:1.5 mL microfuge tube
Tissue Cell Identification:Raji cells


Treatment ID:TR000493
Treatment Summary:Cells were treated with vehicle (dH2O) or 1 ug/mL doxycycline.
Treatment Compound:Doxycycline
Treatment Dose:1 ug/mL
Treatment Dosevolume:10 mL
Treatment Doseduration:0, 48, 96, and 144 hours
Treatment Vehicle:dH2O
Cell Growth Container:T25 Flask
Cell Media Lastchanged:Media changed every two days during time course

Sample Preparation:

Sampleprep ID:SP000486
Sampleprep Summary:Amino acid
Sampleprep Protocol Filename:SB_AA_Assay.pdf

Combined analysis:

Analysis ID AN000719
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1290 Infinity
Column Waters AccQ Tag (100 x 2mm,1.7um)
MS instrument type Triple quadrupole
MS instrument name Agilent 6490 QQQ
Units nmol/mg protein


Chromatography ID:CH000516
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 ID:MS000639
Analysis ID:AN000719
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole