Summary of Study ST000404
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 PR000316. The data can be accessed directly via it's Project DOI: 10.21228/M83P47 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000404 |
| Study Title | Role of HVCN1 in B cell malignancies |
| Study Summary | The proton channel HVCN1 is expressed in B cell malignancies at high levels but its role remains unclear. From initial experiments during which HVCN1 was downregulated in human multiple myeloma cell lines, we observed an increase in some glycolytic and TCA metabolites. We want to get a better idea if HVCN1 is playing a role in regulating energy metabolism in multiple myeloma. |
| Institute | University of California, Davis |
| Department | Genome and Biomedical Sciences Facility |
| Laboratory | WCMC Metabolomics Core |
| Last Name | Fiehn |
| First Name | Oliver |
| Address | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2016-05-26 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | peg |
| Analysis Type Detail | GC-MS |
| Release Date | 2016-06-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000316 |
| Project DOI: | doi: 10.21228/M83P47 |
| Project Title: | Role of HVCN1 in B cell malignancies |
| Project Summary: | The proton channel HVCN1 is expressed in B cell malignancies at high levels but its role remains unclear. From initial experiments during which HVCN1 was downregulated in human multiple myeloma cell lines, we observed an increase in some glycolytic and TCA metabolites. We want to get a better idea if HVCN1 is playing a role in regulating energy metabolism in multiple myeloma. |
| Institute: | University of California, Davis |
| Department: | Genome and Biomedical Sciences Facility |
| Laboratory: | WCMC Metabolomics Core |
| Last Name: | Fiehn |
| First Name: | Oliver |
| Address: | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| Email: | ofiehn@ucdavis.edu |
| Phone: | (530) 754-8258 |
| Funding Source: | NIH U24DK097154 |
Subject:
| Subject ID: | SU000425 |
| Subject Type: | Cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA019348 | 160505dngsa30_2 | clone 5 HVCN1 shRNA |
| SA019349 | 160505dngsa26_1 | clone 5 HVCN1 shRNA |
| SA019350 | 160505dngsa21_2 | clone 5 HVCN1 shRNA |
| SA019351 | 160505dngsa25_2 | clone 5 HVCN1 shRNA |
| SA019352 | 160505dngsa28_2 | clone 6 HVCN1 shRNA |
| SA019353 | 160505dngsa23_1 | clone 6 HVCN1 shRNA |
| SA019354 | 160505dngsa29_2 | clone 6 HVCN1 shRNA |
| SA019355 | 160505dngsa31_1 | clone 6 HVCN1 shRNA |
| SA019344 | 160505dngsa27_2 | Scrambled shRNA |
| SA019345 | 160505dngsa22_3 | Scrambled shRNA |
| SA019346 | 160505dngsa24_1 | Scrambled shRNA |
| SA019347 | 160505dngsa32_1 | Scrambled shRNA |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO000419 |
| Collection Summary: | Cells were harvested and washed in PBS three times before being frozen as cell pellets. |
| Sample Type: | Cells |
Treatment:
| Treatment ID: | TR000439 |
| Treatment Summary: | 3 treatments, 4 samples per treatment group, Treatments are cells with a scrambled shRNA, clone 5 HVCN1 shRNA, clone 6 HVCN1 shRNA |
| Treatment Protocol Filename: | StudyDesignMelaniaCapasso_4.6.2016.pdf |
Sample Preparation:
| Sampleprep ID: | SP000432 |
| Sampleprep Summary: | 1. Add 0.5mL of extraction solvent to tube, gently pipet to remove all cells, transfer cells to 2mL eppendorf tube. Repeat for a total of 1mL extraction solvent + cells in 2mL eppendorf tube. 2. Add 2 small stainless steel grinding beads to eppendorf tube 3. Use the GenoGrinder to grind for 3 minutes at 1,250 rpm. 4. Centrifuge at 14,000xg for 5 minutes. 5. Transfer supernatant to a fresh 2mL eppendorf tube. 6. Add 1mL of extraction solvent to tube containing cell pellet + beads, and repeat steps 3 and 4. 7. Collect supernatant, and combine with supernatant collected in step 5. Total volume of extracted sample will be approximately 2mL. 8. Dry down 50uL of extracted sample in 1.5mL eppendorf tube for GC-TOF analysis. 9. Store backups in -20 or -80C. |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Yeast_Cells.pdf |
Combined analysis:
| Analysis ID | AN000644 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 6890N |
| Column | Restek Corporation Rtx-5Sil MS |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus III GC TOF |
| Ion Mode | POSITIVE |
| Units | counts |
Chromatography:
| Chromatography ID: | CH000468 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf |
| Instrument Name: | Agilent 6890N |
| Column Name: | Restek Corporation Rtx-5Sil MS |
| Column Pressure: | 7.7 PSI |
| Column Temperature: | 50-330C |
| Flow Rate: | 1 ml/min |
| Injection Temperature: | 50 C ramped to 250 C by 12 C/s |
| Sample Injection: | 0.5 uL |
| Oven Temperature: | 50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min |
| Transferline Temperature: | 230C |
| Washing Buffer: | Ethyl Acetate |
| Sample Loop Size: | 30 m length x 0.25 mm internal diameter |
| Randomization Order: | Excel generated |
| Chromatography Type: | GC |
MS:
| MS ID: | MS000576 |
| Analysis ID: | AN000644 |
| Instrument Name: | Leco Pegasus III GC TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 250 C |
| Ionization Energy: | 70 eV |
| Mass Accuracy: | Nominal |
| Source Temperature: | 250 C |
| Scan Range Moverz: | 85-500 Da |
| Scanning Cycle: | 17 Hz |
| Scanning Range: | 85-500 Da |
| Skimmer Voltage: | 1850 V |
