| Project ID | IMP_100037 |
| Title | Lipidomic study of JEV infected MEFs |
| Uploaded by | Manjula |
| Research Area | Biological Sciences |
| Funding Source | ICMR |
| Contributors | Sakshi Khera, Kiran Bala Sharma, Yashwant Kumar, & Manjula Kalia |
| 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. |
| Study ID | IMS_100032 |
| Title | Lipidomic study of JEV infected MEFs |
| Uploaded by | Manjula |
| Study Type | Mass Spectrometry (MS) |
| Data Type | Untargeted |
| Release Date | Aug. 31, 2025 |
| IEC/IBSC No. | RCB/IBSC/21-22/287 |
| Publication | |
| 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. |
| # | Sample ID | Sample Name | Organism | Source | Sample Type | Experimental Condition | Gender | Age | Replicates | Storage | Files/Sample |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | IMSM_101876 | MOCK1 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 2 | IMSM_101877 | MOCK2 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 3 | IMSM_101878 | MOCK3 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 4 | IMSM_101879 | MOCK4 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 5 | IMSM_101880 | MOCK5 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 6 | IMSM_101881 | MOCK6 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 7 | IMSM_101882 | JEV1 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 8 | IMSM_101883 | JEV2 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 9 | IMSM_101884 | JEV3 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 10 | IMSM_101885 | JEV4 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 11 | IMSM_101886 | JEV5 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 12 | IMSM_101887 | JEV6 | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 13 | IMSM_101888 | MOCK1-A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 14 | IMSM_101894 | MOCK2_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 15 | IMSM_101895 | MOCK3_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 16 | IMSM_101896 | MOCK4_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 17 | IMSM_101897 | MOCK5_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 18 | IMSM_101898 | MOCK6_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Untreated | N/A | N/A | NA | -80 | |
| 19 | IMSM_101899 | JEV1_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 20 | IMSM_101900 | JEV2_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 21 | IMSM_101901 | JEV3_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 22 | IMSM_101902 | JEV4_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 23 | IMSM_101903 | JEV5_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 | |
| 24 | IMSM_101904 | JEV6_A | Mus musculus | MEFs (mouse embryonic fibroblasts) | Mouse cells | Infected | N/A | N/A | NA | -80 |
| # | MS Exp ID | Sample Name / ID | MS Type | Instrument Name | Instrument Type | Ionization Method | Ion Mode | Software 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 |
| # | First Name | Last Name | 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 |
| # | FTP Run ID | MS Exp ID | MS Data File |
|---|---|---|---|
| 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 |