Summary of Study ST003116

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 IDST003116
Study TitleComprehensive Untargeted LC-MS Metabolomics Analysis of HMGCS2 Knockout iPSCs(Supernatant/Media)
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:SU003232
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
SA337576HMGCS2_Supernatant_Sample4_HILICneg_SZ_09202023_15iPSC cells CE Basal media (Stemflex)
SA337577HMGCS2_Supernatant_Sample12_HILICneg_SZ_09202023_33iPSC cells CE Basal media (Stemflex)
SA337578HMGCS2_Supernatant_Sample54_RPpos_SZ_09202023_126iPSC cells CE Basal media (Stemflex)
SA337579HMGCS2_Supernatant_Sample54_HILICneg_SZ_09202023_125iPSC cells CE Basal media (Stemflex)
SA337580HMGCS2_Supernatant_Sample53_HILICneg_SZ_09202023_123iPSC cells CE Basal media (Stemflex)
SA337581HMGCS2_Supernatant_Sample45_HILICneg_SZ_09202023_105iPSC cells CE Basal media (Stemflex)
SA337582HMGCS2_Supernatant_Sample48_HILICneg_SZ_09202023_111iPSC cells CE Basal media (Stemflex)
SA337583HMGCS2_Supernatant_Sample22_HILICneg_SZ_09202023_55iPSC cells CE Basal media (Stemflex)
SA337584HMGCS2_Supernatant_Sample12_RPpos_SZ_09202023_34iPSC cells CE Basal media (Stemflex)
SA337585HMGCS2_Supernatant_Sample48_RPpos_SZ_09202023_112iPSC cells CE Basal media (Stemflex)
SA337586HMGCS2_Supernatant_Sample53_RPpos_SZ_09202023_124iPSC cells CE Basal media (Stemflex)
SA337587HMGCS2_Supernatant_Sample45_RPpos_SZ_09202023_106iPSC cells CE Basal media (Stemflex)
SA337588HMGCS2_Supernatant_Sample38_RPpos_SZ_09202023_90iPSC cells CE Basal media (Stemflex)
SA337589HMGCS2_Supernatant_Sample22_RPpos_SZ_09202023_56iPSC cells CE Basal media (Stemflex)
SA337590HMGCS2_Supernatant_Sample35_RPpos_SZ_09202023_84iPSC cells CE Basal media (Stemflex)
SA337591HMGCS2_Supernatant_Sample38_HILICneg_SZ_09202023_89iPSC cells CE Basal media (Stemflex)
SA337592HMGCS2_Supernatant_Sample4_RPpos_SZ_09202023_16iPSC cells CE Basal media (Stemflex)
SA337593HMGCS2_Supernatant_Sample35_HILICneg_SZ_09202023_83iPSC cells CE Basal media (Stemflex)
SA337594HMGCS2_Supernatant_Sample11_HILICneg_SZ_09202023_31iPSC cells CE Complete media (Stemflex + nutrients)
SA337595HMGCS2_Supernatant_Sample9_RPpos_SZ_09202023_26iPSC cells CE Complete media (Stemflex + nutrients)
SA337596HMGCS2_Supernatant_Sample16_HILICneg_SZ_09202023_41iPSC cells CE Complete media (Stemflex + nutrients)
SA337597HMGCS2_Supernatant_Sample26_RPpos_SZ_09202023_64iPSC cells CE Complete media (Stemflex + nutrients)
SA337598HMGCS2_Supernatant_Sample9_HILICneg_SZ_09202023_25iPSC cells CE Complete media (Stemflex + nutrients)
SA337599HMGCS2_Supernatant_Sample11_RPpos_SZ_09202023_32iPSC cells CE Complete media (Stemflex + nutrients)
SA337600HMGCS2_Supernatant_Sample56_HILICneg_SZ_09202023_129iPSC cells CE Complete media (Stemflex + nutrients)
SA337601HMGCS2_Supernatant_Sample16_RPpos_SZ_09202023_42iPSC cells CE Complete media (Stemflex + nutrients)
SA337602HMGCS2_Supernatant_Sample24_RPpos_SZ_09202023_60iPSC cells CE Complete media (Stemflex + nutrients)
SA337603HMGCS2_Supernatant_Sample26_HILICneg_SZ_09202023_63iPSC cells CE Complete media (Stemflex + nutrients)
SA337604HMGCS2_Supernatant_Sample24_HILICneg_SZ_09202023_59iPSC cells CE Complete media (Stemflex + nutrients)
SA337605HMGCS2_Supernatant_Sample7_RPpos_SZ_09202023_22iPSC cells CE Complete media (Stemflex + nutrients)
SA337606HMGCS2_Supernatant_Sample39_HILICneg_SZ_09202023_91iPSC cells CE Complete media (Stemflex + nutrients)
SA337607HMGCS2_Supernatant_Sample41_HILICneg_SZ_09202023_97iPSC cells CE Complete media (Stemflex + nutrients)
SA337608HMGCS2_Supernatant_Sample41_RPpos_SZ_09202023_98iPSC cells CE Complete media (Stemflex + nutrients)
SA337609HMGCS2_Supernatant_Sample56_RPpos_SZ_09202023_130iPSC cells CE Complete media (Stemflex + nutrients)
SA337610HMGCS2_Supernatant_Sample39_RPpos_SZ_09202023_92iPSC cells CE Complete media (Stemflex + nutrients)
SA337611HMGCS2_Supernatant_Sample7_HILICneg_SZ_09202023_21iPSC cells CE Complete media (Stemflex + nutrients)
SA337612HMGCS2_Supernatant_Sample60_RPpos_SZ_09202023_138iPSC cells KO Basal media (Stemflex)
SA337613HMGCS2_Supernatant_Sample8_RPpos_SZ_09202023_24iPSC cells KO Basal media (Stemflex)
SA337614HMGCS2_Supernatant_Sample37_HILICneg_SZ_09202023_87iPSC cells KO Basal media (Stemflex)
SA337615HMGCS2_Supernatant_Sample8_HILICneg_SZ_09202023_23iPSC cells KO Basal media (Stemflex)
SA337616HMGCS2_Supernatant_Sample43_RPpos_SZ_09202023_102iPSC cells KO Basal media (Stemflex)
SA337617HMGCS2_Supernatant_Sample49_RPpos_SZ_09202023_114iPSC cells KO Basal media (Stemflex)
SA337618HMGCS2_Supernatant_Sample37_RPpos_SZ_09202023_88iPSC cells KO Basal media (Stemflex)
SA337619HMGCS2_Supernatant_Sample33_RPpos_SZ_09202023_80iPSC cells KO Basal media (Stemflex)
SA337620HMGCS2_Supernatant_Sample59_RPpos_SZ_09202023_136iPSC cells KO Basal media (Stemflex)
SA337621HMGCS2_Supernatant_Sample29_RPpos_SZ_09202023_70iPSC cells KO Basal media (Stemflex)
SA337622HMGCS2_Supernatant_Sample13_RPpos_SZ_09202023_36iPSC cells KO Basal media (Stemflex)
SA337623HMGCS2_Supernatant_Sample29_HILICneg_SZ_09202023_69iPSC cells KO Basal media (Stemflex)
SA337624HMGCS2_Supernatant_Sample59_HILICneg_SZ_09202023_135iPSC cells KO Basal media (Stemflex)
SA337625HMGCS2_Supernatant_Sample49_HILICneg_SZ_09202023_113iPSC cells KO Basal media (Stemflex)
SA337626HMGCS2_Supernatant_Sample43_HILICneg_SZ_09202023_101iPSC cells KO Basal media (Stemflex)
SA337627HMGCS2_Supernatant_Sample60_HILICneg_SZ_09202023_137iPSC cells KO Basal media (Stemflex)
SA337628HMGCS2_Supernatant_Sample33_HILICneg_SZ_09202023_79iPSC cells KO Basal media (Stemflex)
SA337629HMGCS2_Supernatant_Sample13_HILICneg_SZ_09202023_35iPSC cells KO Basal media (Stemflex)
SA337630HMGCS2_Supernatant_Sample19_HILICneg_SZ_09202023_47iPSC cells KO Complete media (Stemflex + nutrients)
SA337631HMGCS2_Supernatant_Sample20_RPpos_SZ_09202023_50iPSC cells KO Complete media (Stemflex + nutrients)
SA337632HMGCS2_Supernatant_Sample19_RPpos_SZ_09202023_48iPSC cells KO Complete media (Stemflex + nutrients)
SA337633HMGCS2_Supernatant_Sample30_RPpos_SZ_09202023_72iPSC cells KO Complete media (Stemflex + nutrients)
SA337634HMGCS2_Supernatant_Sample47_RPpos_SZ_09202023_110iPSC cells KO Complete media (Stemflex + nutrients)
SA337635HMGCS2_Supernatant_Sample51_HILICneg_SZ_09202023_119iPSC cells KO Complete media (Stemflex + nutrients)
SA337636HMGCS2_Supernatant_Sample20_HILICneg_SZ_09202023_49iPSC cells KO Complete media (Stemflex + nutrients)
SA337637HMGCS2_Supernatant_Sample2_HILICneg_SZ_09202023_11iPSC cells KO Complete media (Stemflex + nutrients)
SA337638HMGCS2_Supernatant_Sample23_RPpos_SZ_09202023_58iPSC cells KO Complete media (Stemflex + nutrients)
SA337639HMGCS2_Supernatant_Sample36_RPpos_SZ_09202023_86iPSC cells KO Complete media (Stemflex + nutrients)
SA337640HMGCS2_Supernatant_Sample51_RPpos_SZ_09202023_120iPSC cells KO Complete media (Stemflex + nutrients)
SA337641HMGCS2_Supernatant_Sample30_HILICneg_SZ_09202023_71iPSC cells KO Complete media (Stemflex + nutrients)
SA337642HMGCS2_Supernatant_Sample36_HILICneg_SZ_09202023_85iPSC cells KO Complete media (Stemflex + nutrients)
SA337643HMGCS2_Supernatant_Sample3_HILICneg_SZ_09202023_13iPSC cells KO Complete media (Stemflex + nutrients)
SA337644HMGCS2_Supernatant_Sample23_HILICneg_SZ_09202023_57iPSC cells KO Complete media (Stemflex + nutrients)
SA337645HMGCS2_Supernatant_Sample3_RPpos_SZ_09202023_14iPSC cells KO Complete media (Stemflex + nutrients)
SA337646HMGCS2_Supernatant_Sample47_HILICneg_SZ_09202023_109iPSC cells KO Complete media (Stemflex + nutrients)
SA337647HMGCS2_Supernatant_Sample2_RPpos_SZ_09202023_12iPSC cells KO Complete media (Stemflex + nutrients)
SA337648HMGCS2_Supernatant_Sample46_RPpos_SZ_09202023_108iPSC cells PTC Basal media (Stemflex)
SA337649HMGCS2_Supernatant_Sample27_HILICneg_SZ_09202023_65iPSC cells PTC Basal media (Stemflex)
SA337650HMGCS2_Supernatant_Sample58_RPpos_SZ_09202023_134iPSC cells PTC Basal media (Stemflex)
SA337651HMGCS2_Supernatant_Sample1_RPpos_SZ_09202023_10iPSC cells PTC Basal media (Stemflex)
SA337652HMGCS2_Supernatant_Sample46_HILICneg_SZ_09202023_107iPSC cells PTC Basal media (Stemflex)
SA337653HMGCS2_Supernatant_Sample27_RPpos_SZ_09202023_66iPSC cells PTC Basal media (Stemflex)
SA337654HMGCS2_Supernatant_Sample1_HILICneg_SZ_09202023_09iPSC cells PTC Basal media (Stemflex)
SA337655HMGCS2_Supernatant_Sample6_HILICneg_SZ_09202023_19iPSC cells PTC Basal media (Stemflex)
SA337656HMGCS2_Supernatant_Sample14_RPpos_SZ_09202023_38iPSC cells PTC Basal media (Stemflex)
SA337657HMGCS2_Supernatant_Sample58_HILICneg_SZ_09202023_133iPSC cells PTC Basal media (Stemflex)
SA337658HMGCS2_Supernatant_Sample18_HILICneg_SZ_09202023_45iPSC cells PTC Basal media (Stemflex)
SA337659HMGCS2_Supernatant_Sample14_HILICneg_SZ_09202023_37iPSC cells PTC Basal media (Stemflex)
SA337660HMGCS2_Supernatant_Sample17_RPpos_SZ_09202023_44iPSC cells PTC Basal media (Stemflex)
SA337661HMGCS2_Supernatant_Sample21_RPpos_SZ_09202023_54iPSC cells PTC Basal media (Stemflex)
SA337662HMGCS2_Supernatant_Sample21_HILICneg_SZ_09202023_53iPSC cells PTC Basal media (Stemflex)
SA337663HMGCS2_Supernatant_Sample6_RPpos_SZ_09202023_20iPSC cells PTC Basal media (Stemflex)
SA337664HMGCS2_Supernatant_Sample18_RPpos_SZ_09202023_46iPSC cells PTC Basal media (Stemflex)
SA337665HMGCS2_Supernatant_Sample17_HILICneg_SZ_09202023_43iPSC cells PTC Basal media (Stemflex)
SA337666HMGCS2_Supernatant_Sample52_RPpos_SZ_09202023_122iPSC cells PTC Complete media (Stemflex + nutrients)
SA337667HMGCS2_Supernatant_Sample44_RPpos_SZ_09202023_104iPSC cells PTC Complete media (Stemflex + nutrients)
SA337668HMGCS2_Supernatant_Sample55_RPpos_SZ_09202023_128iPSC cells PTC Complete media (Stemflex + nutrients)
SA337669HMGCS2_Supernatant_Sample25_HILICneg_SZ_09202023_61iPSC cells PTC Complete media (Stemflex + nutrients)
SA337670HMGCS2_Supernatant_Sample50_RPpos_SZ_09202023_116iPSC cells PTC Complete media (Stemflex + nutrients)
SA337671HMGCS2_Supernatant_Sample52_HILICneg_SZ_09202023_121iPSC cells PTC Complete media (Stemflex + nutrients)
SA337672HMGCS2_Supernatant_Sample55_HILICneg_SZ_09202023_127iPSC cells PTC Complete media (Stemflex + nutrients)
SA337673HMGCS2_Supernatant_Sample34_HILICneg_SZ_09202023_81iPSC cells PTC Complete media (Stemflex + nutrients)
SA337674HMGCS2_Supernatant_Sample32_HILICneg_SZ_09202023_77iPSC cells PTC Complete media (Stemflex + nutrients)
SA337675HMGCS2_Supernatant_Sample5_HILICneg_SZ_09202023_17iPSC cells PTC Complete media (Stemflex + nutrients)
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Collection:

Collection ID:CO003225
Collection Summary:For the media collection, 500ul of media was directly aspirated into 1.5 ml Eppendorf tube from each well and flash frozen with liquid nitrogen, stored immediately at -80 degree C.
Sample Type:iPSC cells

Treatment:

Treatment ID:TR003241
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:SP003239
Sampleprep Summary:See from protocol file.
Sampleprep Protocol Filename:single_phase_mammalian_cellpellet_extraction_Zukai.pdf

Chromatography:

Chromatography ID:CH003864
Methods Filename:Mobilephase_LC_MS_method.pdf
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore HILIC (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:95:5 acetonitrile:water; 10mM ammonium acetate; 0.1% acetic acid
Solvent B:50:50 acetonitrile:water; 10mM ammonium acetate; 0.1% acetic acid
Chromatography Type:HILIC
  
Chromatography ID:CH003865
Methods Filename:Mobilephase_LC_MS_method.pdf
Instrument Name:Thermo Vanquish
Column Name: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% ACN; 0.1% formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN005108
Analysis Type:MS
Analysis Protocol File:Mobilephase_LC_MS_method.pdf
Chromatography ID:CH003864
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST003116_AN005108_Results.txt
Units:peak intensity
  
Analysis ID:AN005109
Analysis Type:MS
Analysis Protocol File:Mobilephase_LC_MS_method.pdf
Chromatography ID:CH003865
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST003116_AN005109_Results.txt
Units:peak intensity
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