Summary of Study ST003115

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001844. The data can be accessed directly via it's Project DOI: 10.21228/M8C145 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST003115
Study TitleComprehensive Untargeted LC-MS Metabolomics Analysis of HMGCS2 Knockout iPSCs(Cell Pellet)
Study SummaryHuman induced pluripotent stem cells (hIPSCs) are a key tool for biomedical research. In this study, human induced pluripotent stem cells of the KOLF2.2J lineage were generated with null allele mutation for HMGCS2. These cell lines were cultured on several types of media with and without various additives and were differentiated into primitive syncytium. Biochemical phenotyping, i.e., untargeted metabolomics and lipidomics profiling, was performed on both differentiated and undifferentiated cells using a Thermo Scientific Q Exactive HF-X Mass Spectrometer coupled to a Thermo Scientific Transcend LX-2 Duo UHPLC system, equipped with an HES-II ionization source, using both positive and negative ionization modes. This dataset, combined with the other -omics level data generated through MorPhiC on these cell lines, provides a molecular foundation for understanding the implications of specific gene deletions in these cell lines and their derivative cell types (e.g., primitive syncytium). This study includes data generated from the cell pellets of the above cell lines. This study was funded, in part, through UM1HG012651 which established the JAX MorPhiC Center, a MorPhiC Phase 1 Data Production Research and Development Center at the Jackson Laboratory for Genomic Medicine.
Institute
Jackson Laboratory for Genomic Medicine
Last NameChi
First NameYuanye
Address10 Discovery Dr, Farmington, CT
Emailyuanye.chi@jax.org
Phone3395456866
Submit Date2024-02-29
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-02-28
Release Version1
Yuanye Chi Yuanye Chi
https://dx.doi.org/10.21228/M8C145
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001844
Project DOI:doi: 10.21228/M8C145
Project Title:Molecular Phenotypes of Null Alleles in Cells
Project Summary:The 2020 NHGRI Strategic Vision laid out a set of “bold predictions for human genomics by 2030” including elucidating the biological function(s) of each human gene. The Molecular Phenotypes of Null Alleles in Cells (MorPhiC) seeks to address this element of the strategic vision. Through the comprehensive generation of null alleles for every human gene and then cataloging the resulting molecular and cellular phenotypes, the mechanisms that relate gene function to observed phenotypes can be determined. Furthermore, the resulting catalog of knockouts and phenotypes will be made available for broader use by the biomedical community. Although multiple approaches can be leveraged to measure molecular and cellular phenotypes resulting from gene knockouts, metabolomics and lipidomics (i.e., biochemical phenotyping) provides an avenue to understand the link between gene function and phenotypes at a molecular level. This project consists of studies performed to biochemical phenotype of cell lines and other samples generated as part of MorPhiC. Resources: 1. https://www.nih.gov/news-events/news-releases/nih-initiative-systematically-investigate-establish-function-every-human-gene 2. https://www.genome.gov/research-funding/Funded-Programs-Projects/Molecular-Phenotypes-of-Null-Alleles-in-Cells
Institute:The Jackson Laboratory for Genomic Medicine
Laboratory:Shuzhao Li Lab
Last Name:Chi
First Name:Yuanye
Address:10 Discovery Dr, Farmington, CT
Email:yuanye.chi@jax.org
Phone:3395456866

Subject:

Subject ID:SU003231
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Sample source KO strategy Media
SA337430HMGCS2_Cellpellets_Sample42_RPpos_SZ_09222023_100iPSC cells CE Basal media (Stemflex)
SA337431HMGCS2_Cellpellets_Sample47_HILICneg_SZ_09222023_109iPSC cells CE Basal media (Stemflex)
SA337432HMGCS2_Cellpellets_Sample42_HILICneg_SZ_09222023_99iPSC cells CE Basal media (Stemflex)
SA337433HMGCS2_Cellpellets_Sample47_RPpos_SZ_09222023_110iPSC cells CE Basal media (Stemflex)
SA337434HMGCS2_Cellpellets_Sample50_RPpos_SZ_09222023_116iPSC cells CE Basal media (Stemflex)
SA337435HMGCS2_Cellpellets_Sample51_HILICneg_SZ_09222023_119iPSC cells CE Basal media (Stemflex)
SA337436HMGCS2_Cellpellets_Sample52_HILICneg_SZ_09222023_121iPSC cells CE Basal media (Stemflex)
SA337437HMGCS2_Cellpellets_Sample26_RPpos_SZ_09222023_64iPSC cells CE Basal media (Stemflex)
SA337438HMGCS2_Cellpellets_Sample30_RPpos_SZ_09222023_72iPSC cells CE Basal media (Stemflex)
SA337439HMGCS2_Cellpellets_Sample38_RPpos_SZ_09222023_90iPSC cells CE Basal media (Stemflex)
SA337440HMGCS2_Cellpellets_Sample53_HILICneg_SZ_09222023_123iPSC cells CE Basal media (Stemflex)
SA337441HMGCS2_Cellpellets_Sample38_HILICneg_SZ_09222023_89iPSC cells CE Basal media (Stemflex)
SA337442HMGCS2_Cellpellets_Sample50_HILICneg_SZ_09222023_115iPSC cells CE Basal media (Stemflex)
SA337443HMGCS2_Cellpellets_Sample52_RPpos_SZ_09222023_122iPSC cells CE Basal media (Stemflex)
SA337444HMGCS2_Cellpellets_Sample26_HILICneg_SZ_09222023_63iPSC cells CE Basal media (Stemflex)
SA337445HMGCS2_Cellpellets_Sample30_HILICneg_SZ_09222023_71iPSC cells CE Basal media (Stemflex)
SA337446HMGCS2_Cellpellets_Sample51_RPpos_SZ_09222023_120iPSC cells CE Basal media (Stemflex)
SA337447HMGCS2_Cellpellets_Sample53_RPpos_SZ_09222023_124iPSC cells CE Basal media (Stemflex)
SA337448HMGCS2_Cellpellets_Sample1_RPpos_SZ_09222023_10iPSC cells CE Complete media (Stemflex + nutrients)
SA337449HMGCS2_Cellpellets_Sample18_HILICneg_SZ_09222023_45iPSC cells CE Complete media (Stemflex + nutrients)
SA337450HMGCS2_Cellpellets_Sample24_RPpos_SZ_09222023_60iPSC cells CE Complete media (Stemflex + nutrients)
SA337451HMGCS2_Cellpellets_Sample19_HILICneg_SZ_09222023_47iPSC cells CE Complete media (Stemflex + nutrients)
SA337452HMGCS2_Cellpellets_Sample24_HILICneg_SZ_09222023_59iPSC cells CE Complete media (Stemflex + nutrients)
SA337453HMGCS2_Cellpellets_Sample1_HILICneg_SZ_09222023_09iPSC cells CE Complete media (Stemflex + nutrients)
SA337454HMGCS2_Cellpellets_Sample34_RPpos_SZ_09222023_82iPSC cells CE Complete media (Stemflex + nutrients)
SA337455HMGCS2_Cellpellets_Sample13_RPpos_SZ_09222023_36iPSC cells CE Complete media (Stemflex + nutrients)
SA337456HMGCS2_Cellpellets_Sample34_HILICneg_SZ_09222023_81iPSC cells CE Complete media (Stemflex + nutrients)
SA337457HMGCS2_Cellpellets_Sample13_HILICneg_SZ_09222023_35iPSC cells CE Complete media (Stemflex + nutrients)
SA337458HMGCS2_Cellpellets_Sample35_RPpos_SZ_09222023_84iPSC cells CE Complete media (Stemflex + nutrients)
SA337459HMGCS2_Cellpellets_Sample7_HILICneg_SZ_09222023_21iPSC cells CE Complete media (Stemflex + nutrients)
SA337460HMGCS2_Cellpellets_Sample6_HILICneg_SZ_09222023_19iPSC cells CE Complete media (Stemflex + nutrients)
SA337461HMGCS2_Cellpellets_Sample35_HILICneg_SZ_09222023_83iPSC cells CE Complete media (Stemflex + nutrients)
SA337462HMGCS2_Cellpellets_Sample7_RPpos_SZ_09222023_22iPSC cells CE Complete media (Stemflex + nutrients)
SA337463HMGCS2_Cellpellets_Sample18_RPpos_SZ_09222023_46iPSC cells CE Complete media (Stemflex + nutrients)
SA337464HMGCS2_Cellpellets_Sample6_RPpos_SZ_09222023_20iPSC cells CE Complete media (Stemflex + nutrients)
SA337465HMGCS2_Cellpellets_Sample19_RPpos_SZ_09222023_48iPSC cells CE Complete media (Stemflex + nutrients)
SA337466HMGCS2_Cellpellets_Sample15_RPpos_SZ_09222023_40iPSC cells KO Basal media (Stemflex)
SA337467HMGCS2_Cellpellets_Sample16_HILICneg_SZ_09222023_41iPSC cells KO Basal media (Stemflex)
SA337468HMGCS2_Cellpellets_Sample15_HILICneg_SZ_09222023_39iPSC cells KO Basal media (Stemflex)
SA337469HMGCS2_Cellpellets_Sample28_RPpos_SZ_09222023_68iPSC cells KO Basal media (Stemflex)
SA337470HMGCS2_Cellpellets_Sample16_RPpos_SZ_09222023_42iPSC cells KO Basal media (Stemflex)
SA337471HMGCS2_Cellpellets_Sample8_RPpos_SZ_09222023_24iPSC cells KO Basal media (Stemflex)
SA337472HMGCS2_Cellpellets_Sample3_RPpos_SZ_09222023_14iPSC cells KO Basal media (Stemflex)
SA337473HMGCS2_Cellpellets_Sample17_RPpos_SZ_09222023_44iPSC cells KO Basal media (Stemflex)
SA337474HMGCS2_Cellpellets_Sample36_RPpos_SZ_09222023_86iPSC cells KO Basal media (Stemflex)
SA337475HMGCS2_Cellpellets_Sample45_RPpos_SZ_09222023_106iPSC cells KO Basal media (Stemflex)
SA337476HMGCS2_Cellpellets_Sample17_HILICneg_SZ_09222023_43iPSC cells KO Basal media (Stemflex)
SA337477HMGCS2_Cellpellets_Sample45_HILICneg_SZ_09222023_105iPSC cells KO Basal media (Stemflex)
SA337478HMGCS2_Cellpellets_Sample28_HILICneg_SZ_09222023_67iPSC cells KO Basal media (Stemflex)
SA337479HMGCS2_Cellpellets_Sample39_HILICneg_SZ_09222023_91iPSC cells KO Basal media (Stemflex)
SA337480HMGCS2_Cellpellets_Sample8_HILICneg_SZ_09222023_23iPSC cells KO Basal media (Stemflex)
SA337481HMGCS2_Cellpellets_Sample3_HILICneg_SZ_09222023_13iPSC cells KO Basal media (Stemflex)
SA337482HMGCS2_Cellpellets_Sample36_HILICneg_SZ_09222023_85iPSC cells KO Basal media (Stemflex)
SA337483HMGCS2_Cellpellets_Sample39_RPpos_SZ_09222023_92iPSC cells KO Basal media (Stemflex)
SA337484HMGCS2_Cellpellets_Sample54_RPpos_SZ_09222023_126iPSC cells KO Complete media (Stemflex + nutrients)
SA337485HMGCS2_Cellpellets_Sample44_RPpos_SZ_09222023_104iPSC cells KO Complete media (Stemflex + nutrients)
SA337486HMGCS2_Cellpellets_Sample23_RPpos_SZ_09222023_58iPSC cells KO Complete media (Stemflex + nutrients)
SA337487HMGCS2_Cellpellets_Sample27_RPpos_SZ_09222023_66iPSC cells KO Complete media (Stemflex + nutrients)
SA337488HMGCS2_Cellpellets_Sample58_RPpos_SZ_09222023_134iPSC cells KO Complete media (Stemflex + nutrients)
SA337489HMGCS2_Cellpellets_Sample40_RPpos_SZ_09222023_94iPSC cells KO Complete media (Stemflex + nutrients)
SA337490HMGCS2_Cellpellets_Sample57_RPpos_SZ_09222023_132iPSC cells KO Complete media (Stemflex + nutrients)
SA337491HMGCS2_Cellpellets_Sample43_RPpos_SZ_09222023_102iPSC cells KO Complete media (Stemflex + nutrients)
SA337492HMGCS2_Cellpellets_Sample10_RPpos_SZ_09222023_28iPSC cells KO Complete media (Stemflex + nutrients)
SA337493HMGCS2_Cellpellets_Sample44_HILICneg_SZ_09222023_103iPSC cells KO Complete media (Stemflex + nutrients)
SA337494HMGCS2_Cellpellets_Sample57_HILICneg_SZ_09222023_131iPSC cells KO Complete media (Stemflex + nutrients)
SA337495HMGCS2_Cellpellets_Sample43_HILICneg_SZ_09222023_101iPSC cells KO Complete media (Stemflex + nutrients)
SA337496HMGCS2_Cellpellets_Sample40_HILICneg_SZ_09222023_93iPSC cells KO Complete media (Stemflex + nutrients)
SA337497HMGCS2_Cellpellets_Sample23_HILICneg_SZ_09222023_57iPSC cells KO Complete media (Stemflex + nutrients)
SA337498HMGCS2_Cellpellets_Sample27_HILICneg_SZ_09222023_65iPSC cells KO Complete media (Stemflex + nutrients)
SA337499HMGCS2_Cellpellets_Sample58_HILICneg_SZ_09222023_133iPSC cells KO Complete media (Stemflex + nutrients)
SA337500HMGCS2_Cellpellets_Sample54_HILICneg_SZ_09222023_125iPSC cells KO Complete media (Stemflex + nutrients)
SA337501HMGCS2_Cellpellets_Sample10_HILICneg_SZ_09222023_27iPSC cells KO Complete media (Stemflex + nutrients)
SA337502HMGCS2_Cellpellets_Sample32_HILICneg_SZ_09222023_77iPSC cells PTC Basal media (Stemflex)
SA337503HMGCS2_Cellpellets_Sample56_HILICneg_SZ_09222023_129iPSC cells PTC Basal media (Stemflex)
SA337504HMGCS2_Cellpellets_Sample20_RPpos_SZ_09222023_50iPSC cells PTC Basal media (Stemflex)
SA337505HMGCS2_Cellpellets_Sample56_RPpos_SZ_09222023_130iPSC cells PTC Basal media (Stemflex)
SA337506HMGCS2_Cellpellets_Sample49_HILICneg_SZ_09222023_113iPSC cells PTC Basal media (Stemflex)
SA337507HMGCS2_Cellpellets_Sample20_HILICneg_SZ_09222023_49iPSC cells PTC Basal media (Stemflex)
SA337508HMGCS2_Cellpellets_Sample9_RPpos_SZ_09222023_26iPSC cells PTC Basal media (Stemflex)
SA337509HMGCS2_Cellpellets_Sample9_HILICneg_SZ_09222023_25iPSC cells PTC Basal media (Stemflex)
SA337510HMGCS2_Cellpellets_Sample49_RPpos_SZ_09222023_114iPSC cells PTC Basal media (Stemflex)
SA337511HMGCS2_Cellpellets_Sample59_HILICneg_SZ_09222023_135iPSC cells PTC Basal media (Stemflex)
SA337512HMGCS2_Cellpellets_Sample32_RPpos_SZ_09222023_78iPSC cells PTC Basal media (Stemflex)
SA337513HMGCS2_Cellpellets_Sample59_RPpos_SZ_09222023_136iPSC cells PTC Basal media (Stemflex)
SA337514HMGCS2_Cellpellets_Sample29_HILICneg_SZ_09222023_69iPSC cells PTC Basal media (Stemflex)
SA337515HMGCS2_Cellpellets_Sample4_HILICneg_SZ_09222023_15iPSC cells PTC Basal media (Stemflex)
SA337516HMGCS2_Cellpellets_Sample25_RPpos_SZ_09222023_62iPSC cells PTC Basal media (Stemflex)
SA337517HMGCS2_Cellpellets_Sample4_RPpos_SZ_09222023_16iPSC cells PTC Basal media (Stemflex)
SA337518HMGCS2_Cellpellets_Sample25_HILICneg_SZ_09222023_61iPSC cells PTC Basal media (Stemflex)
SA337519HMGCS2_Cellpellets_Sample29_RPpos_SZ_09222023_70iPSC cells PTC Basal media (Stemflex)
SA337520HMGCS2_Cellpellets_Sample14_RPpos_SZ_09222023_38iPSC cells PTC Complete media (Stemflex + nutrients)
SA337521HMGCS2_Cellpellets_Sample48_RPpos_SZ_09222023_112iPSC cells PTC Complete media (Stemflex + nutrients)
SA337522HMGCS2_Cellpellets_Sample33_HILICneg_SZ_09222023_79iPSC cells PTC Complete media (Stemflex + nutrients)
SA337523HMGCS2_Cellpellets_Sample46_RPpos_SZ_09222023_108iPSC cells PTC Complete media (Stemflex + nutrients)
SA337524HMGCS2_Cellpellets_Sample21_HILICneg_SZ_09222023_53iPSC cells PTC Complete media (Stemflex + nutrients)
SA337525HMGCS2_Cellpellets_Sample31_HILICneg_SZ_09222023_75iPSC cells PTC Complete media (Stemflex + nutrients)
SA337526HMGCS2_Cellpellets_Sample60_RPpos_SZ_09222023_138iPSC cells PTC Complete media (Stemflex + nutrients)
SA337527HMGCS2_Cellpellets_Sample5_HILICneg_SZ_09222023_17iPSC cells PTC Complete media (Stemflex + nutrients)
SA337528HMGCS2_Cellpellets_Sample46_HILICneg_SZ_09222023_107iPSC cells PTC Complete media (Stemflex + nutrients)
SA337529HMGCS2_Cellpellets_Sample60_HILICneg_SZ_09222023_137iPSC cells PTC Complete media (Stemflex + nutrients)
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Collection:

Collection ID:CO003224
Collection Summary:For the cell collection, wash cells by PBS, place 1ml accutase in each well and incubate at 37 degrees for 7 minutes. After incubation, discard the accutase, wash cells by DPBS, detach cells from bottom of well by cell lifter and then harvest the suspension in 1.5ml Eppendorf tubes. Centrifuge cells for 5 minutes at 300g. Aspirate PBS from the cell pellet and flash freeze cell pellet in liquid nitrogen, store immediately at -80C.
Sample Type:iPSC cells

Treatment:

Treatment ID:TR003240
Treatment Summary:KOLF2.2J cells were passaged as single cells with Accutase and seeded onto SynthemaxII coated 12-well plates at 10k cells per well. 24 h after cell passage, StemFlex media was changed to trophectoderm induction media (TE media). Basal TE media consists of DMEM/F12, supplemented with 20% KnockOut Serum (ThermoFisher, #10828028), 2 mM L-Glutamine (Gibco™, #25030081), 1x MEM non-essential amnio acid (GibcoTM, #11140050), 0.1 mM β-Mercaptoethanol (Sigma, #3148). In addition, 100 ng/ml BMP4 (R&D, #314-BP- 050/CF), and 20 μM SU5402 (Millipore Sigma, # 57263) were added at day 0 and onwards to induce trophoblast lineage (BS condition). For the induction of primitive syncytium, 1 mM A-83 (TOCRIS, #2939) was added at the end of Day 2. Media was refreshed every 2 days until the end of differentiation (Day 6). On day 6, TE media was replaced by the StemFlex media with or without addition of nutrients 24 hours prior to collection.

Sample Preparation:

Sampleprep ID:SP003238
Sampleprep Summary:See from protocol file.
Sampleprep Protocol Filename:single_phase_mammalian_cellpellet_extraction_Zukai.pdf

Chromatography:

Chromatography ID:CH003862
Chromatography Summary:See protocol file
Methods Filename:Mobilephase_LC_MS_method.pdf
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore 150 Amide (100 x 2.1mm, 2.6um)
Column Temperature:45
Flow Gradient:0.0min: 100%A, 0.2min: 2% A, 8.75min: 2%A, 10min: 100%A, 15min: 100%A, 17min: 100%A
Flow Rate:0.55 mL/min
Solvent A:95% acetonitrile5% water; 10mM ammonium acetate; 0.1% acetic acid
Solvent B:50% acetonitrile/50% water; 10mM ammonium acetate; 0.1% acetic acid
Chromatography Type:HILIC
  
Chromatography ID:CH003863
Chromatography Summary:See protocol file
Methods Filename:Mobilephase_LC_MS_method.pdf
Instrument Name:Thermo Vanquish
Column Name:Thermo Hypersil GOLD (50 x 2.1mm, 3um)
Column Temperature:45
Flow Gradient:0.0min: 85%A, 0.01min: 70%A, 2.01min: 52%A, 2.51min: 18%A, 11.0min: 1%A, 11.5min: 1%A, 12.0min: 1%A, 15.0min: 0%A, 16.5min: 85%A, 17.5min: 85%A
Flow Rate:0.4 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN005106
Analysis Type:MS
Analysis Protocol File:Mobilephase_LC_MS_method.pdf
Chromatography ID:CH003862
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST003115_AN005106_Results.txt
Units:peak intensity
  
Analysis ID:AN005107
Analysis Type:MS
Analysis Protocol File:Mobilephase_LC_MS_method.pdf
Chromatography ID:CH003863
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST003115_AN005107_Results.txt
Units:peak intensity
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