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.

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Study IDST000404
Study TitleRole of HVCN1 in B cell malignancies
Study SummaryThe 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
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2016-05-26
Raw Data AvailableYes
Raw Data File Type(s).peg
Analysis Type DetailGC-MS
Release Date2016-06-18
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M83P47
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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:Human

Factors:

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

mb_sample_id local_sample_id Genotype
SA019348160505dngsa30_2clone 5 HVCN1 shRNA
SA019349160505dngsa26_1clone 5 HVCN1 shRNA
SA019350160505dngsa21_2clone 5 HVCN1 shRNA
SA019351160505dngsa25_2clone 5 HVCN1 shRNA
SA019352160505dngsa28_2clone 6 HVCN1 shRNA
SA019353160505dngsa23_1clone 6 HVCN1 shRNA
SA019354160505dngsa29_2clone 6 HVCN1 shRNA
SA019355160505dngsa31_1clone 6 HVCN1 shRNA
SA019344160505dngsa27_2Scrambled shRNA
SA019345160505dngsa22_3Scrambled shRNA
SA019346160505dngsa24_1Scrambled shRNA
SA019347160505dngsa32_1Scrambled 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
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