Summary of Study ST004010

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 PR002511. The data can be accessed directly via it's Project DOI: 10.21228/M82N83 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST004010
Study Title	Measuring the shift in the PC lipididome in HCMV infection timecourse.
Study Summary	The levels of PC lipids are reported to increase in HCMV-infected cells. We measured the shift in the PC lipidome in HCMV infection over a 120 hour time course. We observed that Some PC lipids change in abundance was greater significantly than others. Moreover, We found that HCMV promotes the change in PC lipids beginning between 24 and 48 hpi.
Institute	University of Arizona
Department	Immunobiology
Laboratory	John G. Purdy, PhD
Last Name	Kline
First Name	Ian
Address	805 E 5th St Street
Email	ikline@arizona.edu
Phone	5209092596
Submit Date	2025-06-24
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2025-06-27
Release Version	1

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Project:

Project ID:	PR002511
Project DOI:	doi: 10.21228/M82N83
Project Title:	Measuring the shift in the PC lipididome in HCMV infection timecourse.
Project Summary:	Human cytomegalovirus (HCMV) is a common herpesvirus that establishes a lifelong and persistent infection in its human host. HCMV infection in most people does not cause overt disease. However, in immunocompromised individuals, severe CMV-associated disease can lead to permanent disabilities and even death. Additionally, congenital CMV is the leading infectious cause of birth defects. Viruses have evolved to hijack host metabolic pathways to facilitate their replication cycle. We previously reported HCMV infection increases phosphatidylcholine (PC) lipid levels, including PCs with VLCFAs. To expand upon the previously reported PC phenotype in HCMV infection, we determined the PC lipidome of several infected cell types grown under various growth conditions. Additionally, we determined which host pathways HCMV reprograms to induce PC lipid synthesis and describe when during infection PC lipids changes occur.
Institute:	University of Arizona
Department:	Immunobiology
Laboratory:	John G. Purdy, PhD
Last Name:	Kline
First Name:	Ian
Address:	825 E 5th St Street Tucson, AZ 85719
Email:	ikline@arizona.edu
Phone:	5209092596
Funding Source:	National Institute of Health (NIH) National Institute of Allergy and Infectious Disease (NIAID) R01AI162671, R01AI155539, F32AI178919, and National Institute of Aging (NIA) T32AG058503 award.

Subject:

Subject ID:	SU004148
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male
Cell Strain Details:	HFF
Cell Passage Number:	<30

Factors:

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

mb_sample_id	local_sample_id	Sample source	Time (hpi)	Infection status
SA461638	20191124_pos_TB40E_NT_120hpi_b	Primary human fibroblast cells (HFF)	120	HCMV
SA461639	20191122_pos_TB40E_NT_120hpi_a	Primary human fibroblast cells (HFF)	120	HCMV
SA461640	20191122_pos_TB40E_NT_120hpi_b	Primary human fibroblast cells (HFF)	120	HCMV
SA461641	20191114_pos_TB40E_NT_120hpi_b	Primary human fibroblast cells (HFF)	120	HCMV
SA461642	20191124_pos_TB40E_NT_120hpi_a	Primary human fibroblast cells (HFF)	120	HCMV
SA461643	20191114_pos_TB40E_NT_120hpi_a	Primary human fibroblast cells (HFF)	120	HCMV
SA461644	20191122_pos_mock_NT_120hpi_a	Primary human fibroblast cells (HFF)	120	Uninfected
SA461645	20191114_pos_mock_NT_120hpi_a	Primary human fibroblast cells (HFF)	120	Uninfected
SA461646	20191122_pos_mock_NT_120hpi_b	Primary human fibroblast cells (HFF)	120	Uninfected
SA461647	20191124_pos_mock_NT_120hpi_b	Primary human fibroblast cells (HFF)	120	Uninfected
SA461648	20191124_pos_mock_NT_120hpi_a	Primary human fibroblast cells (HFF)	120	Uninfected
SA461649	20191114_pos_mock_NT_120hpi_b	Primary human fibroblast cells (HFF)	120	Uninfected
SA461650	20191122_pos_TB40E_NT_24hpi_b	Primary human fibroblast cells (HFF)	24	HCMV
SA461651	20191122_pos_TB40E_NT_24hpi_a	Primary human fibroblast cells (HFF)	24	HCMV
SA461652	20191124_pos_TB40E_NT_24hpi_a	Primary human fibroblast cells (HFF)	24	HCMV
SA461653	20191124_pos_TB40E_NT_24hpi_b	Primary human fibroblast cells (HFF)	24	HCMV
SA461654	20191114_pos_TB40E_NT_24hpi_b	Primary human fibroblast cells (HFF)	24	HCMV
SA461655	20191114_pos_TB40E_NT_24hpi_a	Primary human fibroblast cells (HFF)	24	HCMV
SA461656	20191114_pos_mock_NT_24hpi_b	Primary human fibroblast cells (HFF)	24	Uninfected
SA461657	20191114_pos_mock_NT_24hpi_a	Primary human fibroblast cells (HFF)	24	Uninfected
SA461658	20191124_pos_mock_NT_24hpi_a	Primary human fibroblast cells (HFF)	24	Uninfected
SA461659	20191124_pos_mock_NT_24hpi_b	Primary human fibroblast cells (HFF)	24	Uninfected
SA461660	20191122_pos_mock_NT_24hpi_a	Primary human fibroblast cells (HFF)	24	Uninfected
SA461661	20191122_pos_mock_NT_24hpi_b	Primary human fibroblast cells (HFF)	24	Uninfected
SA461662	20191122_pos_TB40E_NT_48hpi_a	Primary human fibroblast cells (HFF)	48	HCMV
SA461663	20191124_pos_TB40E_NT_48hpi_a	Primary human fibroblast cells (HFF)	48	HCMV
SA461664	20191124_pos_TB40E_NT_48hpi_b	Primary human fibroblast cells (HFF)	48	HCMV
SA461665	20191114_pos_TB40E_NT_48hpi_b	Primary human fibroblast cells (HFF)	48	HCMV
SA461666	20191114_pos_TB40E_NT_48hpi_a	Primary human fibroblast cells (HFF)	48	HCMV
SA461667	20191122_pos_TB40E_NT_48hpi_b	Primary human fibroblast cells (HFF)	48	HCMV
SA461668	20191124_pos_mock_NT_48hpi_b	Primary human fibroblast cells (HFF)	48	Uninfected
SA461669	20191114_pos_mock_NT_48hpi_b	Primary human fibroblast cells (HFF)	48	Uninfected
SA461670	20191122_pos_mock_NT_48hpi_b	Primary human fibroblast cells (HFF)	48	Uninfected
SA461671	20191122_pos_mock_NT_48hpi_a	Primary human fibroblast cells (HFF)	48	Uninfected
SA461672	20191124_pos_mock_NT_48hpi_a	Primary human fibroblast cells (HFF)	48	Uninfected
SA461673	20191114_pos_mock_NT_48hpi_a	Primary human fibroblast cells (HFF)	48	Uninfected
SA461674	20191122_pos_TB40E_NT_4hpi_b	Primary human fibroblast cells (HFF)	4	HCMV
SA461675	20191124_pos_TB40E_NT_4hpi_b	Primary human fibroblast cells (HFF)	4	HCMV
SA461676	20191124_pos_TB40E_NT_4hpi_a	Primary human fibroblast cells (HFF)	4	HCMV
SA461677	20191114_pos_TB40E_NT_4hpi_b	Primary human fibroblast cells (HFF)	4	HCMV
SA461678	20191114_pos_TB40E_NT_4hpi_a	Primary human fibroblast cells (HFF)	4	HCMV
SA461679	20191122_pos_TB40E_NT_4hpi_a	Primary human fibroblast cells (HFF)	4	HCMV
SA461680	20191124_pos_mock_NT_4hpi_b	Primary human fibroblast cells (HFF)	4	Uninfected
SA461681	20191124_pos_mock_NT_4hpi_a	Primary human fibroblast cells (HFF)	4	Uninfected
SA461682	20191114_pos_mock_NT_4hpi_a	Primary human fibroblast cells (HFF)	4	Uninfected
SA461683	20191122_pos_mock_NT_4hpi_b	Primary human fibroblast cells (HFF)	4	Uninfected
SA461684	20191114_pos_mock_NT_4hpi_b	Primary human fibroblast cells (HFF)	4	Uninfected
SA461685	20191122_pos_mock_NT_4hpi_a	Primary human fibroblast cells (HFF)	4	Uninfected
SA461686	20191114_pos_TB40E_NT_72hpi_b	Primary human fibroblast cells (HFF)	72	HCMV
SA461687	20191114_pos_TB40E_NT_72hpi_a	Primary human fibroblast cells (HFF)	72	HCMV
SA461688	20191124_pos_TB40E_NT_72hpi_b	Primary human fibroblast cells (HFF)	72	HCMV
SA461689	20191124_pos_TB40E_NT_72hpi_a	Primary human fibroblast cells (HFF)	72	HCMV
SA461690	20191122_pos_TB40E_NT_72hpi_a	Primary human fibroblast cells (HFF)	72	HCMV
SA461691	20191122_pos_TB40E_NT_72hpi_b	Primary human fibroblast cells (HFF)	72	HCMV
SA461692	20191122_pos_mock_NT_72hpi_b	Primary human fibroblast cells (HFF)	72	Uninfected
SA461693	20191114_pos_mock_NT_72hpi_b	Primary human fibroblast cells (HFF)	72	Uninfected
SA461694	20191114_pos_mock_NT_72hpi_a	Primary human fibroblast cells (HFF)	72	Uninfected
SA461695	20191124_pos_mock_NT_72hpi_a	Primary human fibroblast cells (HFF)	72	Uninfected
SA461696	20191124_pos_mock_NT_72hpi_b	Primary human fibroblast cells (HFF)	72	Uninfected
SA461697	20191122_pos_mock_NT_72hpi_a	Primary human fibroblast cells (HFF)	72	Uninfected
SA461698	20191124_pos_TB40E_NT_96hpi_b	Primary human fibroblast cells (HFF)	96	HCMV
SA461699	20191124_pos_TB40E_NT_96hpi_a	Primary human fibroblast cells (HFF)	96	HCMV
SA461700	20191122_pos_TB40E_NT_96hpi_b	Primary human fibroblast cells (HFF)	96	HCMV
SA461701	20191122_pos_TB40E_NT_96hpi_a	Primary human fibroblast cells (HFF)	96	HCMV
SA461702	20191114_pos_TB40E_NT_96hpi_a	Primary human fibroblast cells (HFF)	96	HCMV
SA461703	20191114_pos_TB40E_NT_96hpi_b	Primary human fibroblast cells (HFF)	96	HCMV
SA461704	20191124_pos_mock_NT_96hpi_a	Primary human fibroblast cells (HFF)	96	Uninfected
SA461705	20191124_pos_mock_NT_96hpi_b	Primary human fibroblast cells (HFF)	96	Uninfected
SA461706	20191114_pos_mock_NT_96hpi_b	Primary human fibroblast cells (HFF)	96	Uninfected
SA461707	20191122_pos_mock_NT_96hpi_a	Primary human fibroblast cells (HFF)	96	Uninfected
SA461708	20191122_pos_mock_NT_96hpi_b	Primary human fibroblast cells (HFF)	96	Uninfected
SA461709	20191114_pos_mock_NT_96hpi_a	Primary human fibroblast cells (HFF)	96	Uninfected

Showing results 1 to 72 of 72

Showing results 1 to 72 of 72

Collection:

Collection ID:	CO004141
Collection Summary:	General Notes: -Work over ice when possible (during scraping and between vortex steps etc.). -Chloroform leeches plastics. Avoid contact with plastic caps, tubes and gloves around glass vial tops. -Work in manageable batch numbers. A batch of 8-16 samples at a time is common. -Clean syringes using chloroform before and after collection. Use a unique syringe for each sample (the same syringe can be used if A/B technical replicates are used. Recommend a quick flush of the syringe using 500 μL chloroform before moving from A to B). Begin by counting cell numbers for each sample using a dedicated well meant for MS normalization based on cell count. In a 6-well plate, wash cells 2x with cold PBS. Add 1mL of cold 50% methanol to each well and scrape cells into glass vials. Add 500 μL of chloroform. Vortex on low setting (careful to avoid splashing chloroform onto plastic caps and liners). Centrifuge @1000g for 5 mins. There should be a clear phase separation of methanol and cell debris on top, while the lower phase contains chloroform and lipids. Use a syringe to carefully extract the lower phase without transferring cell debris from the top layer. Transfer to clean vial and place on ice. Once all lipids have been extracted, add 500 μL of chloroform and repeat the process again once more. In total each sample should contain ~1 mL of chloroform and lipids from two extractions. Carefully, dry lipids under nitrogen gas. Avoid direct high pressure air flow onto chloroform:lipid solution as it can splash high up in vial walls. Store at -80℃ for up to 30 days. Samples may become unstable and degrade over time.
Sample Type:	Cultured cells
Collection Location:	Fume hood required when working with chloroform.
Collection Frequency:	Perform extraction twice on each sample.
Collection Duration:	1-2 hours dependent upon batch size
Volumeoramount Collected:	~1 mL chloroform:lipid solution
Storage Conditions:	-80℃
Collection Vials:	Glass vials, no plastic! (plastic cap is okay)
Storage Vials:	Glass vials, no plastic! (plastic cap is okay)
Collection Tube Temp:	25℃

Treatment:

Treatment ID:	TR004157
Treatment Summary:	Cells were grown to full confluence and held for 3-days in Dulbecco's modified eagle medium (DMEM) with 10% fetal bovine serum (FBS). 24 hours prior to infection, cells were starved of serum in DMEM lacking FBS. Cells were HCMV-infected or mock-infected in serum-free DMEM for 1 hour. 1 hpi, cells were maintained in serum-free growth medium. Medium was replaced at 48 hpi.

Sample Preparation:

Sampleprep ID:	SP004154
Sampleprep Summary:	Before starting, calculate the volume of 1:1:1 choloroform:methanol:isopropanol resuspension buffer needed for each sample. Volume of 1:1:1 is dependent on normalize cell count from experiment. Use 200 μL of 1:1:1 for every 2E5 cells. When ready to start resuspension, remove dried lipids from -80℃ storage and resuspend in volume of 1:1:1 solution calculated for each sample. No cell conditions use 200 μL. Use gentle vortex to allow for dried lipids from vial wall to get into solution. Prepare "blank" vials of 1:1:1 for buffer background analysis. Store lipids in autosampler between 4-7℃.

Sampleprep ID:

SP004154

Sampleprep Summary:

Before starting, calculate the volume of 1:1:1 choloroform:methanol:isopropanol resuspension buffer needed for each sample. Volume of 1:1:1 is dependent on normalize cell count from experiment. Use 200 μL of 1:1:1 for every 2E5 cells. When ready to start resuspension, remove dried lipids from -80℃ storage and resuspend in volume of 1:1:1 solution calculated for each sample. No cell conditions use 200 μL. Use gentle vortex to allow for dried lipids from vial wall to get into solution. Prepare "blank" vials of 1:1:1 for buffer background analysis. Store lipids in autosampler between 4-7℃.

Combined analysis:

Analysis ID	AN006614
Chromatography ID	CH005024
MS ID	MS006313
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Thermo Vanquish
Column	Phenomenex Kinetex C18 (100 x 2.1 mm, 2.6 μm)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Orbitrap Exploris 240
Ion Mode	POSITIVE
Units	Peak Area

Chromatography:

Chromatography ID:	CH005024
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (100 x 2.1 mm, 2.6 μm)
Column Temperature:	60℃
Flow Gradient:	75% solvent A–25% solvent B for 2 min, 35% solvent A–65% solvent B for 2min at a curve value of 4, a hold at 35% solvent A–65% solvent B for 1min, 0% solvent A–100% solvent B for 11min at a curve value of 4, and a hold at 0% solvent A–100% solvent B for 4 min.
Flow Rate:	0.25 mL/min
Solvent A:	40% Water/60% Methanol; 10 mM Ammonium formate; 0.1% Formic acid
Solvent B:	10% Methanol/90% Isopropanol; 10 mM Ammonium formate; 0.1% Formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS006313
Analysis ID:	AN006614
Instrument Name:	Thermo Orbitrap Exploris 240
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	PCs were identified in positive mode using parent lipid m/z, RT and choline head fragment of 184.073 m/z. Confirmation of PCs was performed by FA tail analysis in negative mode.
Ion Mode:	POSITIVE