#METABOLOMICS WORKBENCH Yuanye_Chi_20240229_221700 DATATRACK_ID:4682 STUDY_ID:ST003116 ANALYSIS_ID:AN005108
VERSION                          	1
CREATED_ON                       	03-07-2024
#PROJECT
PR:PROJECT_TITLE                 	Molecular Phenotypes of Null Alleles in Cells
PR:PROJECT_SUMMARY               	The 2020 NHGRI Strategic Vision laid out a set of “bold predictions for human
PR:PROJECT_SUMMARY               	genomics by 2030” including elucidating the biological function(s) of each
PR:PROJECT_SUMMARY               	human gene. The Molecular Phenotypes of Null Alleles in Cells (MorPhiC) seeks to
PR:PROJECT_SUMMARY               	address this element of the strategic vision. Through the comprehensive
PR:PROJECT_SUMMARY               	generation of null alleles for every human gene and then cataloging the
PR:PROJECT_SUMMARY               	resulting molecular and cellular phenotypes, the mechanisms that relate gene
PR:PROJECT_SUMMARY               	function to observed phenotypes can be determined. Furthermore, the resulting
PR:PROJECT_SUMMARY               	catalog of knockouts and phenotypes will be made available for broader use by
PR:PROJECT_SUMMARY               	the biomedical community. Although multiple approaches can be leveraged to
PR:PROJECT_SUMMARY               	measure molecular and cellular phenotypes resulting from gene knockouts,
PR:PROJECT_SUMMARY               	metabolomics and lipidomics (i.e., biochemical phenotyping) provides an avenue
PR:PROJECT_SUMMARY               	to understand the link between gene function and phenotypes at a molecular
PR:PROJECT_SUMMARY               	level. This project consists of studies performed to biochemical phenotype of
PR:PROJECT_SUMMARY               	cell lines and other samples generated as part of MorPhiC. Resources: 1.
PR:PROJECT_SUMMARY               	https://www.nih.gov/news-events/news-releases/nih-initiative-systematically-investigate-establish-function-every-human-gene
PR:PROJECT_SUMMARY               	2.
PR:PROJECT_SUMMARY               	https://www.genome.gov/research-funding/Funded-Programs-Projects/Molecular-Phenotypes-of-Null-Alleles-in-Cells
PR:INSTITUTE                     	The Jackson Laboratory for Genomic Medicine
PR:LABORATORY                    	Shuzhao Li Lab
PR:LAST_NAME                     	Chi
PR:FIRST_NAME                    	Yuanye
PR:ADDRESS                       	10 Discovery Dr, Farmington, CT
PR:EMAIL                         	yuanye.chi@jax.org
PR:PHONE                         	3395456866
PR:DOI                           	http://dx.doi.org/10.21228/M8C145
#STUDY
ST:STUDY_TITLE                   	Comprehensive Untargeted LC-MS Metabolomics Analysis of HMGCS2 Knockout
ST:STUDY_TITLE                   	iPSCs(Supernatant/Media)
ST:STUDY_SUMMARY                 	Human induced pluripotent stem cells (hIPSCs) are a key tool for biomedical
ST:STUDY_SUMMARY                 	research. In this study, human induced pluripotent stem cells of the KOLF2.2J
ST:STUDY_SUMMARY                 	lineage were generated with null allele mutation for HMGCS2. These cell lines
ST:STUDY_SUMMARY                 	were cultured on several types of media with and without various additives and
ST:STUDY_SUMMARY                 	were differentiated into primitive syncytium. Biochemical phenotyping, i.e.,
ST:STUDY_SUMMARY                 	untargeted metabolomics and lipidomics profiling, was performed on both
ST:STUDY_SUMMARY                 	differentiated and undifferentiated cells using a Thermo Scientific Q Exactive
ST:STUDY_SUMMARY                 	HF-X Mass Spectrometer coupled to a Thermo Scientific Transcend LX-2 Duo UHPLC
ST:STUDY_SUMMARY                 	system, equipped with an HES-II ionization source, using both positive and
ST:STUDY_SUMMARY                 	negative ionization modes. This dataset, combined with the other -omics level
ST:STUDY_SUMMARY                 	data generated through MorPhiC on these cell lines, provides a molecular
ST:STUDY_SUMMARY                 	foundation for understanding the implications of specific gene deletions in
ST:STUDY_SUMMARY                 	these cell lines and their derivative cell types (e.g., primitive syncytium).
ST:STUDY_SUMMARY                 	This study includes data generated from the cell pellets of the above cell
ST:STUDY_SUMMARY                 	lines. This study was funded, in part, through UM1HG012651 which established the
ST:STUDY_SUMMARY                 	JAX MorPhiC Center, a MorPhiC Phase 1 Data Production Research and Development
ST:STUDY_SUMMARY                 	Center at the Jackson Laboratory for Genomic Medicine.
ST:INSTITUTE                     	The Jackson Laboratory for Genomic Medicine
ST:LAST_NAME                     	Chi
ST:FIRST_NAME                    	Yuanye
ST:ADDRESS                       	10 Discovery Dr, Farmington, CT
ST:EMAIL                         	yuanye.chi@jax.org
ST:PHONE                         	3395456866
ST:SUBMIT_DATE                   	2024-02-29
#SUBJECT
SU:SUBJECT_TYPE                  	Human
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample12_HILICneg_SZ_09202023_33	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample12_HILICneg_SZ_09202023_33.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample12_RPpos_SZ_09202023_34	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample12_RPpos_SZ_09202023_34.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample22_HILICneg_SZ_09202023_55	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample22_HILICneg_SZ_09202023_55.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample22_RPpos_SZ_09202023_56	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample22_RPpos_SZ_09202023_56.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample35_HILICneg_SZ_09202023_83	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample35_HILICneg_SZ_09202023_83.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample35_RPpos_SZ_09202023_84	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample35_RPpos_SZ_09202023_84.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample38_HILICneg_SZ_09202023_89	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample38_HILICneg_SZ_09202023_89.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample38_RPpos_SZ_09202023_90	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample38_RPpos_SZ_09202023_90.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample45_HILICneg_SZ_09202023_105	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample45_HILICneg_SZ_09202023_105.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample45_RPpos_SZ_09202023_106	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample45_RPpos_SZ_09202023_106.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample48_HILICneg_SZ_09202023_111	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample48_HILICneg_SZ_09202023_111.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample48_RPpos_SZ_09202023_112	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample48_RPpos_SZ_09202023_112.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample4_HILICneg_SZ_09202023_15	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample4_HILICneg_SZ_09202023_15.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample4_RPpos_SZ_09202023_16	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample4_RPpos_SZ_09202023_16.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample53_HILICneg_SZ_09202023_123	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample53_HILICneg_SZ_09202023_123.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample53_RPpos_SZ_09202023_124	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample53_RPpos_SZ_09202023_124.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample54_HILICneg_SZ_09202023_125	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample54_HILICneg_SZ_09202023_125.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample54_RPpos_SZ_09202023_126	Sample source:iPSC cells | KO strategy:CE | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample54_RPpos_SZ_09202023_126.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample11_HILICneg_SZ_09202023_31	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample11_HILICneg_SZ_09202023_31.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample11_RPpos_SZ_09202023_32	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample11_RPpos_SZ_09202023_32.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample16_HILICneg_SZ_09202023_41	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample16_HILICneg_SZ_09202023_41.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample16_RPpos_SZ_09202023_42	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample16_RPpos_SZ_09202023_42.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample24_HILICneg_SZ_09202023_59	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample24_HILICneg_SZ_09202023_59.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample24_RPpos_SZ_09202023_60	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample24_RPpos_SZ_09202023_60.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample26_HILICneg_SZ_09202023_63	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample26_HILICneg_SZ_09202023_63.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample26_RPpos_SZ_09202023_64	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample26_RPpos_SZ_09202023_64.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample39_HILICneg_SZ_09202023_91	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample39_HILICneg_SZ_09202023_91.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample39_RPpos_SZ_09202023_92	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample39_RPpos_SZ_09202023_92.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample41_HILICneg_SZ_09202023_97	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample41_HILICneg_SZ_09202023_97.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample41_RPpos_SZ_09202023_98	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample41_RPpos_SZ_09202023_98.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample56_HILICneg_SZ_09202023_129	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample56_HILICneg_SZ_09202023_129.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample56_RPpos_SZ_09202023_130	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample56_RPpos_SZ_09202023_130.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample7_HILICneg_SZ_09202023_21	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample7_HILICneg_SZ_09202023_21.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample7_RPpos_SZ_09202023_22	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample7_RPpos_SZ_09202023_22.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample9_HILICneg_SZ_09202023_25	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample9_HILICneg_SZ_09202023_25.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample9_RPpos_SZ_09202023_26	Sample source:iPSC cells | KO strategy:CE | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample9_RPpos_SZ_09202023_26.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample13_HILICneg_SZ_09202023_35	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample13_HILICneg_SZ_09202023_35.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample13_RPpos_SZ_09202023_36	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample13_RPpos_SZ_09202023_36.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample29_HILICneg_SZ_09202023_69	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample29_HILICneg_SZ_09202023_69.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample29_RPpos_SZ_09202023_70	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample29_RPpos_SZ_09202023_70.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample33_HILICneg_SZ_09202023_79	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample33_HILICneg_SZ_09202023_79.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample33_RPpos_SZ_09202023_80	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample33_RPpos_SZ_09202023_80.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample37_HILICneg_SZ_09202023_87	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample37_HILICneg_SZ_09202023_87.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample37_RPpos_SZ_09202023_88	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample37_RPpos_SZ_09202023_88.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample43_HILICneg_SZ_09202023_101	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample43_HILICneg_SZ_09202023_101.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample43_RPpos_SZ_09202023_102	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample43_RPpos_SZ_09202023_102.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample49_HILICneg_SZ_09202023_113	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample49_HILICneg_SZ_09202023_113.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample49_RPpos_SZ_09202023_114	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample49_RPpos_SZ_09202023_114.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample59_HILICneg_SZ_09202023_135	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample59_HILICneg_SZ_09202023_135.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample59_RPpos_SZ_09202023_136	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample59_RPpos_SZ_09202023_136.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample60_HILICneg_SZ_09202023_137	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample60_HILICneg_SZ_09202023_137.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample60_RPpos_SZ_09202023_138	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample60_RPpos_SZ_09202023_138.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample8_HILICneg_SZ_09202023_23	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample8_HILICneg_SZ_09202023_23.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample8_RPpos_SZ_09202023_24	Sample source:iPSC cells | KO strategy:KO | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample8_RPpos_SZ_09202023_24.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample19_HILICneg_SZ_09202023_47	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample19_HILICneg_SZ_09202023_47.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample19_RPpos_SZ_09202023_48	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample19_RPpos_SZ_09202023_48.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample20_HILICneg_SZ_09202023_49	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample20_HILICneg_SZ_09202023_49.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample20_RPpos_SZ_09202023_50	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample20_RPpos_SZ_09202023_50.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample23_HILICneg_SZ_09202023_57	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample23_HILICneg_SZ_09202023_57.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample23_RPpos_SZ_09202023_58	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample23_RPpos_SZ_09202023_58.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample2_HILICneg_SZ_09202023_11	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample2_HILICneg_SZ_09202023_11.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample2_RPpos_SZ_09202023_12	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample2_RPpos_SZ_09202023_12.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample30_HILICneg_SZ_09202023_71	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample30_HILICneg_SZ_09202023_71.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample30_RPpos_SZ_09202023_72	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample30_RPpos_SZ_09202023_72.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample36_HILICneg_SZ_09202023_85	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample36_HILICneg_SZ_09202023_85.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample36_RPpos_SZ_09202023_86	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample36_RPpos_SZ_09202023_86.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample3_HILICneg_SZ_09202023_13	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample3_HILICneg_SZ_09202023_13.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample3_RPpos_SZ_09202023_14	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample3_RPpos_SZ_09202023_14.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample47_HILICneg_SZ_09202023_109	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample47_HILICneg_SZ_09202023_109.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample47_RPpos_SZ_09202023_110	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample47_RPpos_SZ_09202023_110.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample51_HILICneg_SZ_09202023_119	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample51_HILICneg_SZ_09202023_119.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample51_RPpos_SZ_09202023_120	Sample source:iPSC cells | KO strategy:KO | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample51_RPpos_SZ_09202023_120.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample14_HILICneg_SZ_09202023_37	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample14_HILICneg_SZ_09202023_37.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample14_RPpos_SZ_09202023_38	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample14_RPpos_SZ_09202023_38.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample17_HILICneg_SZ_09202023_43	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample17_HILICneg_SZ_09202023_43.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample17_RPpos_SZ_09202023_44	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample17_RPpos_SZ_09202023_44.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample18_HILICneg_SZ_09202023_45	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample18_HILICneg_SZ_09202023_45.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample18_RPpos_SZ_09202023_46	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample18_RPpos_SZ_09202023_46.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample1_HILICneg_SZ_09202023_09	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample1_HILICneg_SZ_09202023_09.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample1_RPpos_SZ_09202023_10	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample1_RPpos_SZ_09202023_10.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample21_HILICneg_SZ_09202023_53	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample21_HILICneg_SZ_09202023_53.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample21_RPpos_SZ_09202023_54	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample21_RPpos_SZ_09202023_54.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample27_HILICneg_SZ_09202023_65	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample27_HILICneg_SZ_09202023_65.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample27_RPpos_SZ_09202023_66	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample27_RPpos_SZ_09202023_66.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample46_HILICneg_SZ_09202023_107	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample46_HILICneg_SZ_09202023_107.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample46_RPpos_SZ_09202023_108	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample46_RPpos_SZ_09202023_108.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample58_HILICneg_SZ_09202023_133	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample58_HILICneg_SZ_09202023_133.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample58_RPpos_SZ_09202023_134	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample58_RPpos_SZ_09202023_134.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample6_HILICneg_SZ_09202023_19	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample6_HILICneg_SZ_09202023_19.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample6_RPpos_SZ_09202023_20	Sample source:iPSC cells | KO strategy:PTC | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample6_RPpos_SZ_09202023_20.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample25_HILICneg_SZ_09202023_61	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample25_HILICneg_SZ_09202023_61.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample25_RPpos_SZ_09202023_62	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample25_RPpos_SZ_09202023_62.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample31_HILICneg_SZ_09202023_75	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample31_HILICneg_SZ_09202023_75.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample31_RPpos_SZ_09202023_76	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample31_RPpos_SZ_09202023_76.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample32_HILICneg_SZ_09202023_77	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample32_HILICneg_SZ_09202023_77.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample32_RPpos_SZ_09202023_78	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample32_RPpos_SZ_09202023_78.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample34_HILICneg_SZ_09202023_81	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample34_HILICneg_SZ_09202023_81.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample34_RPpos_SZ_09202023_82	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample34_RPpos_SZ_09202023_82.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample44_HILICneg_SZ_09202023_103	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample44_HILICneg_SZ_09202023_103.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample44_RPpos_SZ_09202023_104	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample44_RPpos_SZ_09202023_104.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample50_HILICneg_SZ_09202023_115	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample50_HILICneg_SZ_09202023_115.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample50_RPpos_SZ_09202023_116	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample50_RPpos_SZ_09202023_116.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample52_HILICneg_SZ_09202023_121	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample52_HILICneg_SZ_09202023_121.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample52_RPpos_SZ_09202023_122	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample52_RPpos_SZ_09202023_122.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample55_HILICneg_SZ_09202023_127	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample55_HILICneg_SZ_09202023_127.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample55_RPpos_SZ_09202023_128	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample55_RPpos_SZ_09202023_128.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample5_HILICneg_SZ_09202023_17	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample5_HILICneg_SZ_09202023_17.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample5_RPpos_SZ_09202023_18	Sample source:iPSC cells | KO strategy:PTC | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample5_RPpos_SZ_09202023_18.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample10_HILICneg_SZ_09202023_27	Sample source:iPSC cells | KO strategy:WT | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample10_HILICneg_SZ_09202023_27.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample10_RPpos_SZ_09202023_28	Sample source:iPSC cells | KO strategy:WT | Media:Basal media (Stemflex)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample10_RPpos_SZ_09202023_28.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample28_HILICneg_SZ_09202023_67	Sample source:iPSC cells | KO strategy:WT | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample28_HILICneg_SZ_09202023_67.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample28_RPpos_SZ_09202023_68	Sample source:iPSC cells | KO strategy:WT | Media:Basal media (Stemflex)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample28_RPpos_SZ_09202023_68.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample40_HILICneg_SZ_09202023_93	Sample source:iPSC cells | KO strategy:WT | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample40_HILICneg_SZ_09202023_93.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample40_RPpos_SZ_09202023_94	Sample source:iPSC cells | KO strategy:WT | Media:Basal media (Stemflex)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample40_RPpos_SZ_09202023_94.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample15_HILICneg_SZ_09202023_39	Sample source:iPSC cells | KO strategy:WT | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample15_HILICneg_SZ_09202023_39.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample15_RPpos_SZ_09202023_40	Sample source:iPSC cells | KO strategy:WT | Media:Complete media (Stemflex + nutrients)	Replicates=2; RAW_FILE_NAME=HMGCS2_Supernatant_Sample15_RPpos_SZ_09202023_40.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample42_HILICneg_SZ_09202023_99	Sample source:iPSC cells | KO strategy:WT | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample42_HILICneg_SZ_09202023_99.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample42_RPpos_SZ_09202023_100	Sample source:iPSC cells | KO strategy:WT | Media:Complete media (Stemflex + nutrients)	Replicates=1; RAW_FILE_NAME=HMGCS2_Supernatant_Sample42_RPpos_SZ_09202023_100.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample57_HILICneg_SZ_09202023_131	Sample source:iPSC cells | KO strategy:WT | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample57_HILICneg_SZ_09202023_131.mzML
SUBJECT_SAMPLE_FACTORS           	-	HMGCS2_Supernatant_Sample57_RPpos_SZ_09202023_132	Sample source:iPSC cells | KO strategy:WT | Media:Complete media (Stemflex + nutrients)	Replicates=3; RAW_FILE_NAME=HMGCS2_Supernatant_Sample57_RPpos_SZ_09202023_132.mzML
SUBJECT_SAMPLE_FACTORS           	-	Process_blank_HMGCS2_Supernatant_1_HILICneg_SZ_09202023_03	Sample source:Process_Blank | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Process_blank_HMGCS2_Supernatant_1_HILICneg_SZ_09202023_03.mzML
SUBJECT_SAMPLE_FACTORS           	-	Process_blank_HMGCS2_Supernatant_1_RPpos_SZ_09202023_04	Sample source:Process_Blank | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Process_blank_HMGCS2_Supernatant_1_RPpos_SZ_09202023_04.mzML
SUBJECT_SAMPLE_FACTORS           	-	Process_blank_HMGCS2_Supernatant_2_HILICneg_SZ_09202023_143	Sample source:Process_Blank | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Process_blank_HMGCS2_Supernatant_2_HILICneg_SZ_09202023_143.mzML
SUBJECT_SAMPLE_FACTORS           	-	Process_blank_HMGCS2_Supernatant_2_RPpos_SZ_09202023_144	Sample source:Process_Blank | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Process_blank_HMGCS2_Supernatant_2_RPpos_SZ_09202023_144.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_HILICneg_1_SZ_09202023_07	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_HILICneg_1_SZ_09202023_07.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_HILICneg_2_SZ_09202023_29	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_HILICneg_2_SZ_09202023_29.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_HILICneg_3_SZ_09202023_51	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_HILICneg_3_SZ_09202023_51.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_HILICneg_4_SZ_09202023_73	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_HILICneg_4_SZ_09202023_73.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_HILICneg_5_SZ_09202023_95	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_HILICneg_5_SZ_09202023_95.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_HILICneg_6_SZ_09202023_117	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_HILICneg_6_SZ_09202023_117.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_HILICneg_7_SZ_09202023_139	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_HILICneg_7_SZ_09202023_139.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_RPpos_1_SZ_09202023_08	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_RPpos_1_SZ_09202023_08.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_RPpos_2_SZ_09202023_30	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_RPpos_2_SZ_09202023_30.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_RPpos_3_SZ_09202023_52	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_RPpos_3_SZ_09202023_52.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_RPpos_4_SZ_09202023_74	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_RPpos_4_SZ_09202023_74.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_RPpos_5_SZ_09202023_96	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_RPpos_5_SZ_09202023_96.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_RPpos_6_SZ_09202023_118	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_RPpos_6_SZ_09202023_118.mzML
SUBJECT_SAMPLE_FACTORS           	-	Pool_QC_HMGCS2_Supernatant_RPpos_7_SZ_09202023_140	Sample source:QC | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Pool_QC_HMGCS2_Supernatant_RPpos_7_SZ_09202023_140.mzML
SUBJECT_SAMPLE_FACTORS           	-	Qstd_HILICneg_1_SZ_09202023_05	Sample source:Qstd | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Qstd_HILICneg_1_SZ_09202023_05.mzML
SUBJECT_SAMPLE_FACTORS           	-	Qstd_HILICneg_2_SZ_09202023_141	Sample source:Qstd | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Qstd_HILICneg_2_SZ_09202023_141.mzML
SUBJECT_SAMPLE_FACTORS           	-	Qstd_RPpos_1_SZ_09202023_06	Sample source:Qstd | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Qstd_RPpos_1_SZ_09202023_06.mzML
SUBJECT_SAMPLE_FACTORS           	-	Qstd_RPpos_2_SZ_09202023_142	Sample source:Qstd | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Qstd_RPpos_2_SZ_09202023_142.mzML
SUBJECT_SAMPLE_FACTORS           	-	Solvent_blank_MobileA1B1_1_RPpos_SZ_09202023_02	Sample source:Solvent_Blank | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Solvent_blank_MobileA1B1_1_RPpos_SZ_09202023_02.mzML
SUBJECT_SAMPLE_FACTORS           	-	Solvent_blank_MobileA1B1_2_RPpos_SZ_09202023_146	Sample source:Solvent_Blank | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Solvent_blank_MobileA1B1_2_RPpos_SZ_09202023_146.mzML
SUBJECT_SAMPLE_FACTORS           	-	Solvent_blank_MobileA2B2_1_HILICneg_SZ_09202023_01	Sample source:Solvent_Blank | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Solvent_blank_MobileA2B2_1_HILICneg_SZ_09202023_01.mzML
SUBJECT_SAMPLE_FACTORS           	-	Solvent_blank_MobileA2B2_2_HILICneg_SZ_09202023_145	Sample source:Solvent_Blank | KO strategy:- | Media:-	Replicates=-; RAW_FILE_NAME=Solvent_blank_MobileA2B2_2_HILICneg_SZ_09202023_145.mzML
#COLLECTION
CO:COLLECTION_SUMMARY            	For the media collection, 500ul of media was directly aspirated into 1.5 ml
CO:COLLECTION_SUMMARY            	Eppendorf tube from each well and flash frozen with liquid nitrogen, stored
CO:COLLECTION_SUMMARY            	immediately at -80 degree C.
CO:SAMPLE_TYPE                   	iPSC cells
#TREATMENT
TR:TREATMENT_SUMMARY             	KOLF2.2J cells were passaged as single cells with Accutase and seeded onto
TR:TREATMENT_SUMMARY             	SynthemaxII coated 12-well plates at 10k cells per well. 24 h after cell
TR:TREATMENT_SUMMARY             	passage, StemFlex media was changed to trophectoderm induction media (TE media).
TR:TREATMENT_SUMMARY             	Basal TE media consists of DMEM/F12, supplemented with 20% KnockOut Serum
TR:TREATMENT_SUMMARY             	(ThermoFisher, #10828028), 2 mM L-Glutamine (Gibco™, #25030081), 1x MEM
TR:TREATMENT_SUMMARY             	non-essential amnio acid (GibcoTM, #11140050), 0.1 mM β-Mercaptoethanol (Sigma,
TR:TREATMENT_SUMMARY             	#3148). In addition, 100 ng/ml BMP4 (R&D, #314-BP- 050/CF), and 20 μM SU5402
TR:TREATMENT_SUMMARY             	(Millipore Sigma, # 57263) were added at day 0 and onwards to induce trophoblast
TR:TREATMENT_SUMMARY             	lineage (BS condition). For the induction of primitive syncytium, 1 mM A-83
TR:TREATMENT_SUMMARY             	(TOCRIS, #2939) was added at the end of Day 2. Media was refreshed every 2 days
TR:TREATMENT_SUMMARY             	until the end of differentiation (Day 6). On day 6, TE media was replaced by the
TR:TREATMENT_SUMMARY             	StemFlex media with or without addition of nutrients 24 hours prior to
TR:TREATMENT_SUMMARY             	collection.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	See from protocol file.
SP:SAMPLEPREP_PROTOCOL_FILENAME  	single_phase_mammalian_cellpellet_extraction_Zukai.pdf
#CHROMATOGRAPHY
CH:METHODS_FILENAME              	Mobilephase_LC_MS_method.pdf
CH:INSTRUMENT_NAME               	Thermo Vanquish
CH:COLUMN_NAME                   	Thermo Accucore HILIC (100 x 2.1mm,2.6um)
CH:COLUMN_TEMPERATURE            	45
CH:FLOW_GRADIENT                 	0.0min: 100%A, 0.2min: 2% A, 8.75min: 2%A, 10min: 100%A, 15min: 100%A, 17min:
CH:FLOW_GRADIENT                 	100%A
CH:FLOW_RATE                     	0.55 mL/min
CH:SOLVENT_A                     	95:5 acetonitrile:water; 10mM ammonium acetate; 0.1% acetic acid
CH:SOLVENT_B                     	50:50 acetonitrile:water; 10mM ammonium acetate; 0.1% acetic acid
CH:CHROMATOGRAPHY_TYPE           	HILIC
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
AN:ANALYSIS_PROTOCOL_FILE        	Mobilephase_LC_MS_method.pdf
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive HF-X Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:MS_COMMENTS                   	See from Protocol file.
MS:ION_MODE                      	NEGATIVE
MS:MS_RESULTS_FILE               	ST003116_AN005108_Results.txt	UNITS:peak intensity	Has m/z:Yes	Has RT:Yes	RT units:Seconds
#END