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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000459 |
| Study Title | Effect of Odc knockout on amino acid steady state levels of Eμ-Myc lymphomas |
| Study Type | Cells are treated with vehicle or Doxycycline - to promote deletion of Odc gene |
| Study Summary | Cells were collected 48 hours after treatment with Dox. |
| Institute | University of Florida |
| Department | SECIM |
| Laboratory | John Cleveland |
| Last Name | Fernandez |
| First Name | Mario |
| Address | 12902 Magnolia Drive, MRC 4-West |
| mario.fernandez@moffitt.org | |
| Phone | 813-745-5140 |
| Submit Date | 2016-09-08 |
| Num Groups | 4 |
| Total Subjects | 12 |
| Study Comments | Groups collected in triplicate per time point, either treated or untreated with Doxycycline. |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-07-08 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | Mammal |
Factors:
Subject type: Cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Genotype |
|---|---|---|---|
| SA023229 | YA95_11 | Doxycycline | Odc -/- |
| SA023230 | YA95_10 | Doxycycline | Odc -/- |
| SA023231 | YA95_12 | Doxycycline | Odc -/- |
| SA023232 | YA95_6 | Doxycycline | Odc WT |
| SA023233 | YA95_4 | Doxycycline | Odc WT |
| SA023234 | YA95_5 | Doxycycline | Odc WT |
| SA023235 | YA95_9 | Vehicle | Odc WT |
| SA023236 | YA95_7 | Vehicle | Odc WT |
| SA023237 | YA95_2 | Vehicle | Odc WT |
| SA023238 | YA95_3 | Vehicle | Odc WT |
| SA023239 | YA95_1 | Vehicle | Odc WT |
| SA023240 | YA95_8 | Vehicle | 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 |
