#METABOLOMICS WORKBENCH KaminiMagon_20230118_094509 DATATRACK_ID:3693 STUDY_ID:ST002448 ANALYSIS_ID:AN003992 PROJECT_ID:PR001579 VERSION 1 CREATED_ON January 19, 2023, 2:09 pm #PROJECT PR:PROJECT_TITLE Identifying how human papillomavirus (HPV) 18 establishment alters metabolism in PR:PROJECT_TITLE primary human foreskin keratinocytes PR:PROJECT_SUMMARY HPV18 is a causative agent of many cancers at a range of anatomical sites. PR:PROJECT_SUMMARY However, the development of cancer often takes many years following initial PR:PROJECT_SUMMARY infection and requires the virus to be able to persist and replicate within the PR:PROJECT_SUMMARY host. Measuring metabolic changes immediately after HPV18 establishment will PR:PROJECT_SUMMARY enable early metabolic changes associated with HPV18 persistence to be PR:PROJECT_SUMMARY determined. Here, we compare the metabolic profiles of HPV18 genome-containing PR:PROJECT_SUMMARY primary human foreskin keratinocytes from six donors, compared to donor-matched PR:PROJECT_SUMMARY untransfected controls. The aim was to identify metabolic and lipid changes PR:PROJECT_SUMMARY associated with HPV establishment in primary human foreskin keratinocytes. PR:INSTITUTE University of Birmingham, UK PR:DEPARTMENT Institute of Cancer and Genomic Sciences PR:LAST_NAME Parish PR:FIRST_NAME Joanna PR:ADDRESS IBR Wolfson Drive Medical School PR:EMAIL J.L.Parish@bham.ac.uk PR:PHONE +44 (0)121 415 8151 #STUDY ST:STUDY_TITLE Metabolic analysis of primary HPV18-genome containing human foreskin ST:STUDY_TITLE keratinocytes compared to untransfected donor-matched controls. ST:STUDY_SUMMARY Six primary HPV18-genome containing human foreskin keratinocyte cell populations ST:STUDY_SUMMARY and six donor-matched primary untransfected human foreskin keratinocyte cell ST:STUDY_SUMMARY populations were grown on lethally-irradiated 3T3-J2 fibroblasts. Before ST:STUDY_SUMMARY harvesting the keratinocytes, the 3T3-J2 fibroblasts were washed off. Cells and ST:STUDY_SUMMARY spent media were harvested and frozen at -80°C until processing. ST:INSTITUTE University of Birmingham, UK ST:DEPARTMENT Institute of Cancer and Genomic Sciences ST:LABORATORY Joanna Parish ST:LAST_NAME Parish ST:FIRST_NAME Joanna ST:ADDRESS IBR Wolfson Drive Medical School, University of Birmingham, Edgbaston ST:EMAIL J.L.Parish@bham.ac.uk ST:PHONE +44 (0)121 415 8151 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 12 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:CELL_STRAIN_DETAILS Primary human foreskin keratinocytes SU:CELL_PRIMARY_IMMORTALIZED Primary #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - CHES_4_CON_cells_HIL_NEG HPV Status:control Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=CHES_4_CON_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - CHES_3_HPV_cells_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=CHES_3_HPV_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - BER_6_HPV_cells_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=BER_6_HPV_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - BER_5_CON_cells_HIL_NEG HPV Status:control Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=BER_5_CON_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - OLI_12_CON_cells_HIL_NEG HPV Status:control Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=OLI_12_CON_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - OLI_11_HPV_cells_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=OLI_11_HPV_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - HAR_2_HPV_cells_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=HAR_2_HPV_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - HAR_1_CON_cells_HIL_NEG HPV Status:control Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=HAR_1_CON_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - CLO_9_CON_cells_HIL_NEG HPV Status:control Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=CLO_9_CON_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - CLO_10_HPV_cells_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=CLO_10_HPV_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - GEO_7_HPV_cells_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=GEO_7_HPV_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - GEO_8_CON_cells_HIL_NEG HPV Status:control Experimental Condition=HILIC Cells Negative Ion; RAW_FILE_NAME=GEO_8_CON_cells_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - CHES_4_CON_cells_HIL_POS HPV Status:control Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=CHES_4_CON_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - CHES_3_HPV_cells_HIL_POS HPV Status:HPV Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=CHES_3_HPV_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - BER_6_HPV_cells_HIL_POS HPV Status:HPV Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=BER_6_HPV_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - BER_5_CON_cells_HIL_POS HPV Status:control Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=BER_5_CON_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - OLI_12_CON_cells_HIL_POS HPV Status:control Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=OLI_12_CON_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - OLI_11_HPV_cells_HIL_POS HPV Status:HPV Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=OLI_11_HPV_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - HAR_2_HPV_cells_HIL_POS HPV Status:HPV Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=HAR_2_HPV_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - HAR_1_CON_cells_HIL_POS HPV Status:control Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=HAR_1_CON_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - CLO_9_CON_cells_HIL_POS HPV Status:control Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=CLO_9_CON_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - CLO_10_HPV_cells_HIL_POS HPV Status:HPV Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=CLO_10_HPV_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - GEO_7_HPV_cells_HIL_POS HPV Status:HPV Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=GEO_7_HPV_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - GEO_8_CON_cells_HIL_POS HPV Status:control Experimental Condition=HILIC Cells Positive Ion; RAW_FILE_NAME=GEO_8_CON_cells_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - CHES_4_CON_media_HIL_NEG HPV Status:control Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=CHES_4_CON_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - CHES_3_HPV_media_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=CHES_3_HPV_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - BER_6_HPV_media_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=BER_6_HPV_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - BER_5_CON_media_HIL_NEG HPV Status:control Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=BER_5_CON_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - OLI_12_CON_media_HIL_NEG HPV Status:control Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=OLI_12_CON_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - OLI_11_HPV_media_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=OLI_11_HPV_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - HAR_2_HPV_media_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=HAR_2_HPV_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - HAR_1_CON_media_HIL_NEG HPV Status:control Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=HAR_1_CON_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - CLO_9_CON_media_HIL_NEG HPV Status:control Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=CLO_9_CON_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - CLO_10_HPV_media_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=CLO_10_HPV_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - GEO_7_HPV_media_HIL_NEG HPV Status:HPV Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=GEO_7_HPV_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - GEO_8_CON_media_HIL_NEG HPV Status:control Experimental Condition=HILIC Media Negative Ion; RAW_FILE_NAME=GEO_8_CON_media_HIL_NEG.mzML SUBJECT_SAMPLE_FACTORS - CHES_4_CON_media_HIL_POS HPV Status:control Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=CHES_4_CON_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - CHES_3_HPV_media_HIL_POS HPV Status:HPV Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=CHES_3_HPV_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - BER_6_HPV_media_HIL_POS HPV Status:HPV Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=BER_6_HPV_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - BER_5_CON_media_HIL_POS HPV Status:control Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=BER_5_CON_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - OLI_12_CON_media_HIL_POS HPV Status:control Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=OLI_12_CON_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - OLI_11_HPV_media_HIL_POS HPV Status:HPV Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=OLI_11_HPV_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - HAR_2_HPV_media_HIL_POS HPV Status:HPV Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=HAR_2_HPV_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - HAR_1_CON_media_HIL_POS HPV Status:control Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=HAR_1_CON_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - CLO_9_CON_media_HIL_POS HPV Status:control Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=CLO_9_CON_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - CLO_10_HPV_media_HIL_POS HPV Status:HPV Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=CLO_10_HPV_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - GEO_7_HPV_media_HIL_POS HPV Status:HPV Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=GEO_7_HPV_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - GEO_8_CON_media_HIL_POS HPV Status:control Experimental Condition=HILIC Media Positive Ion; RAW_FILE_NAME=GEO_8_CON_media_HIL_POS.mzML SUBJECT_SAMPLE_FACTORS - CHES_4_CON_cells_LIP_NEG HPV Status:control Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=CHES_4_CON_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - CHES_3_HPV_cells_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=CHES_3_HPV_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - BER_6_HPV_cells_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=BER_6_HPV_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - BER_5_CON_cells_LIP_NEG HPV Status:control Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=BER_5_CON_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - OLI_12_CON_cells_LIP_NEG HPV Status:control Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=OLI_12_CON_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - OLI_11_HPV_cells_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=OLI_11_HPV_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - HAR_2_HPV_cells_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=HAR_2_HPV_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - HAR_1_CON_cells_LIP_NEG HPV Status:control Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=HAR_1_CON_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - CLO_9_CON_cells_LIP_NEG HPV Status:control Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=CLO_9_CON_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - CLO_10_HPV_cells_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=CLO_10_HPV_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - GEO_7_HPV_cells_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=GEO_7_HPV_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - GEO_8_CON_cells_LIP_NEG HPV Status:control Experimental Condition=Lipids Intracellular Negative Ion; RAW_FILE_NAME=GEO_8_CON_cells_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - CHES_4_CON_cells_LIP_POS HPV Status:control Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=CHES_4_CON_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - CHES_3_HPV_cells_LIP_POS HPV Status:HPV Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=CHES_3_HPV_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - BER_6_HPV_cells_LIP_POS HPV Status:HPV Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=BER_6_HPV_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - BER_5_CON_cells_LIP_POS HPV Status:control Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=BER_5_CON_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - OLI_12_CON_cells_LIP_POS HPV Status:control Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=OLI_12_CON_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - OLI_11_HPV_cells_LIP_POS HPV Status:HPV Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=OLI_11_HPV_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - HAR_2_HPV_cells_LIP_POS HPV Status:HPV Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=HAR_2_HPV_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - HAR_1_CON_cells_LIP_POS HPV Status:control Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=HAR_1_CON_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - CLO_9_CON_cells_LIP_POS HPV Status:control Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=CLO_9_CON_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - CLO_10_HPV_cells_LIP_POS HPV Status:HPV Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=CLO_10_HPV_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - GEO_7_HPV_cells_LIP_POS HPV Status:HPV Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=GEO_7_HPV_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - GEO_8_CON_cells_LIP_POS HPV Status:control Experimental Condition=Lipids Intracellular Positive Ion; RAW_FILE_NAME=GEO_8_CON_cells_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - CHES_4_CON_media_LIP_NEG HPV Status:control Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=CHES_4_CON_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - CHES_3_HPV_media_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=CHES_3_HPV_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - BER_6_HPV_media_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=BER_6_HPV_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - BER_5_CON_media_LIP_NEG HPV Status:control Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=BER_5_CON_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - OLI_12_CON_media_LIP_NEG HPV Status:control Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=OLI_12_CON_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - OLI_11_HPV_media_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=OLI_11_HPV_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - HAR_2_HPV_media_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=HAR_2_HPV_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - HAR_1_CON_media_LIP_NEG HPV Status:control Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=HAR_1_CON_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - CLO_9_CON_media_LIP_NEG HPV Status:control Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=CLO_9_CON_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - CLO_10_HPV_media_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=CLO_10_HPV_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - GEO_7_HPV_media_LIP_NEG HPV Status:HPV Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=GEO_7_HPV_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - GEO_8_CON_media_LIP_NEG HPV Status:control Experimental Condition=Lipids Media Negative Ion; RAW_FILE_NAME=GEO_8_CON_media_LIP_NEG.mzML SUBJECT_SAMPLE_FACTORS - CHES_4_CON_media_LIP_POS HPV Status:control Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=CHES_4_CON_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - CHES_3_HPV_media_LIP_POS HPV Status:HPV Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=CHES_3_HPV_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - BER_6_HPV_media_LIP_POS HPV Status:HPV Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=BER_6_HPV_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - BER_5_CON_media_LIP_POS HPV Status:control Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=BER_5_CON_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - OLI_12_CON_media_LIP_POS HPV Status:control Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=OLI_12_CON_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - OLI_11_HPV_media_LIP_POS HPV Status:HPV Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=OLI_11_HPV_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - HAR_2_HPV_media_LIP_POS HPV Status:HPV Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=HAR_2_HPV_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - HAR_1_CON_media_LIP_POS HPV Status:control Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=HAR_1_CON_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - CLO_9_CON_media_LIP_POS HPV Status:control Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=CLO_9_CON_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - CLO_10_HPV_media_LIP_POS HPV Status:HPV Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=CLO_10_HPV_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - GEO_7_HPV_media_LIP_POS HPV Status:HPV Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=GEO_7_HPV_media_LIP_POS.mzML SUBJECT_SAMPLE_FACTORS - GEO_8_CON_media_LIP_POS HPV Status:control Experimental Condition=Lipids Media Positive Ion; RAW_FILE_NAME=GEO_8_CON_media_LIP_POS.mzML #COLLECTION CO:COLLECTION_SUMMARY Adherent cells were washed in saline, frozen in the 6-well plate and stored at CO:COLLECTION_SUMMARY -80°C. Spent media was taken, frozen and stored at -80°C. CO:SAMPLE_TYPE Keratinocytes #TREATMENT TR:TREATMENT_SUMMARY Normal primary HFKs from neonatal foreskin epithelia were transfected with TR:TREATMENT_SUMMARY recircularised HPV18 wild type. All cells were grown in the presence of TR:TREATMENT_SUMMARY irradiated 3T3-J2 fibroblasts. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Metabolite and lipid extraction from cells and resuspension for UHPLC-MS SP:SAMPLEPREP_SUMMARY Metabolites and lipids were extracted from cells in 6-well plates using a SP:SAMPLEPREP_SUMMARY biphasic methanol/chloroform/water method. 6-well plates were placed on dry ice SP:SAMPLEPREP_SUMMARY and 600 uL ice-cold methanol/water solution (ratio 2/0.8, LC-MS grade, Fisher) SP:SAMPLEPREP_SUMMARY was added. Cells were dislodged into the liquid using a cell scraper (Corning) SP:SAMPLEPREP_SUMMARY and then all liquid and cells were removed into a clean 1.8 mL glass vial SP:SAMPLEPREP_SUMMARY (Wheaton). A further 240 μL methanol/water solution (ratio 2/0.8) was added to SP:SAMPLEPREP_SUMMARY the same well, scraped again and the liquid and cells were added to the 1.8 mL SP:SAMPLEPREP_SUMMARY glass vial. 600 uL chloroform and 300 uL water (both LC-MS grade, Fisher) were SP:SAMPLEPREP_SUMMARY added to the glass vial. Sample was vortexed (30 s), incubated on ice (10 min) SP:SAMPLEPREP_SUMMARY and centrifuged (2,500-g, 10 min, 4oC). The sample was set at room temperature SP:SAMPLEPREP_SUMMARY for 5 min to allow phase partitioning to complete. All the polar (upper) phase SP:SAMPLEPREP_SUMMARY was removed into a 2 mL microfuge tube (Eppendorf) and dried in a SpeedVac SP:SAMPLEPREP_SUMMARY concentrator (Savant SPD111V230, Thermo Fisher Scientific). All the non-polar SP:SAMPLEPREP_SUMMARY (lower) phase was removed into a 2 mL microfuge tube (Eppendorf) and dried on a SP:SAMPLEPREP_SUMMARY nitrogen blow down drier (Techne FSC400D, Thermo Fisher Scientific). To create SP:SAMPLEPREP_SUMMARY process blank samples, the entire process was done in the absence of cellular SP:SAMPLEPREP_SUMMARY material. Polar samples were reconstituted in 120 uL 3/1 acetonitrile /water SP:SAMPLEPREP_SUMMARY (all LC-MS grade, VWR) and non-polar samples reconstituted in 3/1 SP:SAMPLEPREP_SUMMARY isopropanol/water (all LC-MS grade, Merck). Each sample was vortexed (15 s), SP:SAMPLEPREP_SUMMARY centrifuged (20,000-g, 20 min, 4oC) and 80 uL of the supernatant loaded into a SP:SAMPLEPREP_SUMMARY low recovery HPLC vial (Chromatography Direct, UK). Quality control (QC) samples SP:SAMPLEPREP_SUMMARY were created by pooling 20 uL from each biological samples and then vortexing SP:SAMPLEPREP_SUMMARY (30 s) before distributing across 5 low recovery HPLC vials. Metabolite and SP:SAMPLEPREP_SUMMARY lipid extraction from media samples For the extraction of polar metabolites, 150 SP:SAMPLEPREP_SUMMARY µL of ice-cold acetonitrile (LC-MS grade, Fisher) was added to 50 µL of media. SP:SAMPLEPREP_SUMMARY Each sample was vortexed (15 s), centrifuged (20,000-g, 20 min, 4oC) and 80 uL SP:SAMPLEPREP_SUMMARY of the supernatant loaded into a low recovery HPLC vial (Chromatography Direct, SP:SAMPLEPREP_SUMMARY UK). For the extraction of non-polar metabolites, 150 µL of ice-cold SP:SAMPLEPREP_SUMMARY isopropanol (LC-MS grade, Fisher) was added to 50 µL of media. Each sample was SP:SAMPLEPREP_SUMMARY vortexed (15 s), centrifuged (20,000-g, 20 min, 4oC) and 80 uL of the SP:SAMPLEPREP_SUMMARY supernatant loaded into a low recovery HPLC vial (Chromatography Direct, UK). QC SP:SAMPLEPREP_SUMMARY samples were prepared by pooling 50 uL from each media sample, vortexing (30 s), SP:SAMPLEPREP_SUMMARY and then distributing 50 uL aliquots across several 2 mL microfuge tubes SP:SAMPLEPREP_SUMMARY (Eppendorf). Process blank samples were prepared by adding 50 uL LC-MS grade SP:SAMPLEPREP_SUMMARY water to 2 mL microfuge tubes. QC and process blank samples were extracted as SP:SAMPLEPREP_SUMMARY for samples (above) for polar and non-polar metabolites separately. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY HILIC assays used an Accucore150-Amide-HILIC column (100×2.1mm, 2.6μm, CH:CHROMATOGRAPHY_SUMMARY ThermoFisher Scientific). Mobile phase A was 10 mM ammonium formate dissolved in CH:CHROMATOGRAPHY_SUMMARY acetonitrile/water/formic acid (95:4.9:0.1 (v/v) and mobile phase B was 10 mM CH:CHROMATOGRAPHY_SUMMARY ammonium formate dissolved in acetonitrile/water/formic acid (50/49.9/0.1 CH:CHROMATOGRAPHY_SUMMARY (v/v)). The gradient elution applied was t=0.0, 1% B; t=1.0, 1% B; t=3.0, 15% B; CH:CHROMATOGRAPHY_SUMMARY t=6.0, 50% B; t=9.0, 95% B; t=10.0, 95% B; t=10.5, 1% B; t=14.0, 1% B. All CH:CHROMATOGRAPHY_SUMMARY changes were linear (curve = 5) and the flow rate was 0.50 mL/min. Column CH:CHROMATOGRAPHY_SUMMARY temperature was 35 °C and injection volume was 2μL. Data were acquired in CH:CHROMATOGRAPHY_SUMMARY positive and negative ionisation mode separately (70 – 1050 m/z) with a mass CH:CHROMATOGRAPHY_SUMMARY resolution 70,000 (FWHM, m/z 200). Ion source parameters: Sheath gas = 55 CH:CHROMATOGRAPHY_SUMMARY arbitrary units, Aux gas = 35 arbitrary units, Sweep gas = 4 arbitrary units, CH:CHROMATOGRAPHY_SUMMARY Spray Voltage = 3.2kV (positive ion) / 2.7kV (negative ion), Capillary temp. = CH:CHROMATOGRAPHY_SUMMARY 380°C, Aux gas heater temp. = 440°C. Thermo ExactiveTune (2.8 SP1, build 2806) CH:CHROMATOGRAPHY_SUMMARY software controlled the instruments and data acquisition. All data were acquired CH:CHROMATOGRAPHY_SUMMARY in profile mode. CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Thermo Dionex Ultimate 3000 CH:COLUMN_NAME Thermo Accucore HILIC (50 x 2.1mm,2.6um) CH:SOLVENT_A 95% acetonitrile/5% water; 0.1% formic acid; 10 mM ammonium formate CH:SOLVENT_B 50% acetonitrile/50% water; 0.1% formic acid; 10 mM ammonium formate CH:FLOW_GRADIENT gradient elution applied was t=0.0, 1% B; t=1.0, 1% B; t=3.0, 15% B; t=6.0, 50% CH:FLOW_GRADIENT B; t=9.0, 95% B; t=10.0, 95% B; t=10.5, 1% B; t=14.0, 1% B. All changes were CH:FLOW_GRADIENT linear (curve = 5) CH:FLOW_RATE 0.50 mL/min CH:COLUMN_TEMPERATURE 35 °C #ANALYSIS AN:ANALYSIS_TYPE MS #MS #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY HILIC assays used an Accucore150-Amide-HILIC column (100×2.1mm, 2.6μm, CH:CHROMATOGRAPHY_SUMMARY ThermoFisher Scientific). Mobile phase A was 10 mM ammonium formate dissolved in CH:CHROMATOGRAPHY_SUMMARY acetonitrile/water/formic acid (95:4.9:0.1 (v/v) and mobile phase B was 10 mM CH:CHROMATOGRAPHY_SUMMARY ammonium formate dissolved in acetonitrile/water/formic acid (50/49.9/0.1 CH:CHROMATOGRAPHY_SUMMARY (v/v)). The gradient elution applied was t=0.0, 1% B; t=1.0, 1% B; t=3.0, 15% B; CH:CHROMATOGRAPHY_SUMMARY t=6.0, 50% B; t=9.0, 95% B; t=10.0, 95% B; t=10.5, 1% B; t=14.0, 1% B. All CH:CHROMATOGRAPHY_SUMMARY changes were linear (curve = 5) and the flow rate was 0.50 mL/min. Column CH:CHROMATOGRAPHY_SUMMARY temperature was 35 °C and injection volume was 2μL. Data were acquired in CH:CHROMATOGRAPHY_SUMMARY positive and negative ionisation mode separately (70 – 1050 m/z) with a mass CH:CHROMATOGRAPHY_SUMMARY resolution 70,000 (FWHM, m/z 200). Ion source parameters: Sheath gas = 55 CH:CHROMATOGRAPHY_SUMMARY arbitrary units, Aux gas = 35 arbitrary units, Sweep gas = 4 arbitrary units, CH:CHROMATOGRAPHY_SUMMARY Spray Voltage = 3.2kV (positive ion) / 2.7kV (negative ion), Capillary temp. = CH:CHROMATOGRAPHY_SUMMARY 380°C, Aux gas heater temp. = 440°C. Thermo ExactiveTune (2.8 SP1, build 2806) CH:CHROMATOGRAPHY_SUMMARY software controlled the instruments and data acquisition. All data were acquired CH:CHROMATOGRAPHY_SUMMARY in profile mode. CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Thermo Dionex Ultimate 3000 CH:COLUMN_NAME Thermo Accucore HILIC (50 x 2.1mm,2.6um) CH:SOLVENT_A 95% acetonitrile/5% water; 0.1% formic acid; 10 mM ammonium formate CH:SOLVENT_B 50% acetonitrile/50% water; 0.1% formic acid; 10 mM ammonium formate CH:FLOW_GRADIENT gradient elution applied was t=0.0, 1% B; t=1.0, 1% B; t=3.0, 15% B; t=6.0, 50% CH:FLOW_GRADIENT B; t=9.0, 95% B; t=10.0, 95% B; t=10.5, 1% B; t=14.0, 1% B. All changes were CH:FLOW_GRADIENT linear (curve = 5) CH:FLOW_RATE 0.50 mL/min CH:COLUMN_TEMPERATURE 35 °C #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Focus MS:ION_MODE POSITIVE MS:MS_COMMENTS All samples were analyzed applying two UHPLC−MS methods (HILIC [polar MS:MS_COMMENTS metabolites] and Lipid [non-polar metabolites] assay, see below) in positive and MS:MS_COMMENTS negative ion modes separately using a Dionex UltiMate 3000 UHPLC system coupled MS:MS_COMMENTS with a heated electrospray Q Exactive Focus mass spectrometer (Thermo Fisher MS:MS_COMMENTS Scientific). QC samples were analysed as the ten of the first eleven injections MS:MS_COMMENTS (to condition the analytical platform) and then every seventh injection was a QC MS:MS_COMMENTS sample with two QC samples injected at the end of the analytical batch. An MS:MS_COMMENTS extract blank sample was analysed as the fifth injection and then the last MS:MS_COMMENTS injection of each batch. All data were collected as MS1 data in profile mode MS:MS_COMMENTS with the exception of QC sample injections where MS/MS data were collected in MS:MS_COMMENTS the “Discovery mode” setting over different precursor m/z ranges (HILIC: MS:MS_COMMENTS 70−200 m/z, 200−400 m/z, 400−1000 m/z; lipids: 150−650 m/z; 650−750 MS:MS_COMMENTS m/z; 750−850 m/z; 850−950 m/z; 950−2000 m/z) using stepped collision MS:MS_COMMENTS energies (HILIC positive ion mode: 20, 40, 100 eV; HILIC negative ion mode: 40, MS:MS_COMMENTS 60, 130 eV; lipids positive ion mode: 20, 40, 100 eV; lipids negative ion mode: MS:MS_COMMENTS 40, 60, 130 eV). All samples were maintained at a temperature of 4°C during the MS:MS_COMMENTS analytical batch. MS:MS_RESULTS_FILE ST002448_AN003992_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Seconds #END