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MS Study

Project uploaded by: Manjula
Project ID: IMP_100037
Title: Lipidomic study of JEV infected MEFs
Project Description: This study was conducted to investigate the impact of JEV infection on the lipid metabolic profile in MEFs. Using LC-MS/MS analysis, we observed significant dysregulation of lipid species in infected cells compared to mock-treated cells. Specifically, there was a reduction in cholesterol, diacylglycerols (DAGs), triacylglycerols (TAGs), and cholesterol esters, alongside an increase in phospholipid species and ceramides. These findings suggested that targeting the cholesterol biosynthesis pathway may serve as a potential antiviral strategy against JEV infection.
Research Area: Biological Sciences
Funding Source: ICMR
Project Contributors: Sakshi Khera, Kiran Bala Sharma, Yashwant Kumar, & Manjula Kalia

Study uploaded by: Manjula
Study ID: IMS_100032
Title: Lipidomic study of JEV infected MEFs
Summary: We identified a total of 840 lipid species, mainly belonging to carnitines, sterols, sphingolipids, phospholipids, glycerolipids, ceramides, sphingomyelins, and plasmalogens. JEV infection dysregulated approximately 41% of the total identified lipidome. Major changes were seen in the abundance of sterols, sphingolipids, phospholipids, glycerolipids and plasmalogens. Among the phospholipid subclasses, PC, PS, PI, and PG, as well as ceramides and plasmalogens (except plasmanyl-TG), were found to be increased in the infected cells, whereas the levels of sterols, glycerolipids, and plasmanyl-TG were reduced during infection. Further analysis of cholesterol biosynthesis pathway genes revealed a transcriptional downregulation of their expression, where Dhcr7 showed the most pronounced reduction of nearly 50% in virus-infected MEFs and BMDMs, suggesting that JEV infection results in a coordinated downregulation of the cholesterol biosynthetic pathway and a decrease in cholesterol levels in infected cells.
Publication:
Release Date: Aug. 31, 2025
Study Type: Mass Spectrometry (MS)
Data Type: Untargeted
IEC/IBSC Approval Number : RCB/IBSC/21-22/287

Sr.No Sample ID Sample Name Organism Source Sample Preparation Protocol Sample Type Experimental Condition Time of treatment Variant/Variety Gender Age Replicates Storage Conditions Extraction Protocol Number of files per sample
1 IMSM_101876 MOCK1 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
2 IMSM_101877 MOCK2 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
3 IMSM_101878 MOCK3 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
4 IMSM_101879 MOCK4 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
5 IMSM_101880 MOCK5 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
6 IMSM_101881 MOCK6 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
7 IMSM_101882 JEV1 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
8 IMSM_101883 JEV2 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
9 IMSM_101884 JEV3 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
10 IMSM_101885 JEV4 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
11 IMSM_101886 JEV5 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
12 IMSM_101887 JEV6 Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
13 IMSM_101888 MOCK1-A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
14 IMSM_101894 MOCK2_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
15 IMSM_101895 MOCK3_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
16 IMSM_101896 MOCK4_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
17 IMSM_101897 MOCK5_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
18 IMSM_101898 MOCK6_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Untreated N/A N/A N/A N/A NA -80

UPLC
19 IMSM_101899 JEV1_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
20 IMSM_101900 JEV2_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
21 IMSM_101901 JEV3_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
22 IMSM_101902 JEV4_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
23 IMSM_101903 JEV5_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC
24 IMSM_101904 JEV6_A Mus musculus Mus musculus Samples were prepared in methanol followed by sonication and addition of MTBE (methyl-tert-butyl ether) Mouse cells Infected N/A N/A N/A N/A NA -80

UPLC

Sr.No MS Exp ID Sample Name/ID Mass Spectrometer Type MS Instrument Name MS Instrument type MS Ionization Method Ion Mode/Scan Polarity Data Transformation (Software/s Used)
1 IME_101121 MOCK1 / IMSM_101876 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
2 IME_101122 MOCK1-A / IMSM_101888 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
3 IME_101123 MOCK2_A / IMSM_101894 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
4 IME_101124 MOCK3_A / IMSM_101895 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
5 IME_101125 MOCK4_A / IMSM_101896 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
6 IME_101126 MOCK5_A / IMSM_101897 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
7 IME_101127 MOCK6_A / IMSM_101898 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
8 IME_101128 JEV1_A / IMSM_101899 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
9 IME_101129 JEV2_A / IMSM_101900 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
10 IME_101130 JEV3_A / IMSM_101901 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
11 IME_101131 JEV4_A / IMSM_101902 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
12 IME_101132 JEV5_A / IMSM_101903 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
13 IME_101133 JEV6_A / IMSM_101904 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
14 IME_101134 MOCK2 / IMSM_101877 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
15 IME_101135 MOCK3 / IMSM_101878 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
16 IME_101136 MOCK4 / IMSM_101879 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
17 IME_101137 MOCK5 / IMSM_101880 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
18 IME_101138 MOCK6 / IMSM_101881 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
19 IME_101139 JEV1 / IMSM_101882 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
20 IME_101140 JEV2 / IMSM_101883 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
21 IME_101141 JEV3 / IMSM_101884 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
22 IME_101142 JEV4 / IMSM_101885 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
23 IME_101143 JEV5 / IMSM_101886 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst
24 IME_101144 JEV6 / IMSM_101887 LCMS (Liquid Chromatography- Mass Spectrometry) Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Orbitrap Electrospray ionization source (ESI) Positive and negative Metabolanalyst

Sr.No First name Last name Email Organization Designation
1 Manjula Kalia manjula@rcb.res.in RCB principal_investigator
2 Yashwant Kumar y.kumar@thsti.res.in THSTI scientist
3 Kiran Bala Sharma kiranjnu91@gmail.com Umeå Universitet postdoctoral_researcher
4 Sakshi Khera sakshi.khera@rcb.res.in Regional Centre for Biotechnology research_scholar

Sr.No ftprun ID MS Exp ID MS Data Files
1 IMR_101720 IME_101121 MK_1_NEG.raw
2 IMR_101726 IME_101122 MK_1_POS.raw
3 IMR_101727 IME_101123 MK_2_POS.raw
4 IMR_101728 IME_101124 MK_3_POS.raw
5 IMR_101729 IME_101125 MK_4_POS.raw
6 IMR_101730 IME_101126 MK_5_POS.raw
7 IMR_101731 IME_101127 MK_6_POS.raw
8 IMR_101732 IME_101128 MK_7_POS.raw
9 IMR_101733 IME_101129 MK_8_POS.raw
10 IMR_101734 IME_101130 MK_9_POS.raw
11 IMR_101735 IME_101131 MK_10_POS.raw
12 IMR_101736 IME_101132 MK_11_POS.raw
13 IMR_101737 IME_101133 MK_12_POS.raw
14 IMR_101738 IME_101134 MK_2_NEG.raw
15 IMR_101739 IME_101135 MK_3_NEG.raw
16 IMR_101740 IME_101136 MK_4_NEG.raw
17 IMR_101741 IME_101137 MK_5_NEG.raw
18 IMR_101742 IME_101138 MK_6_NEG.raw
19 IMR_101743 IME_101139 MK_7_NEG.raw
20 IMR_101744 IME_101140 MK_8_NEG.raw
21 IMR_101745 IME_101141 MK_9_NEG.raw
22 IMR_101746 IME_101142 MK_10_NEG.raw
23 IMR_101747 IME_101143 MK_11_NEG.raw
24 IMR_101748 IME_101144 MK_12_NEG.raw

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