Summary of Study ST003952

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 IDST003952
Study TitleComprehensive Untargeted LC-MS Metabolomics Analysis of STS/HSD3B1 Knockout iPSCs (supernatant)
Study SummaryHuman induced pluripotent stem cells (hIPSCs) are a key tool for biomedical research. Using CRISPR-cas9, null mutations were generated in KOLF2.2J hIPSCs and subsequently differentiated into primitive syncytium. In this study, null allele mutations were generated in STS and HSD3B1, genes encoding key enzymes in the steroidogenesis pathway. Cells were cultured on media with and without DHEA-S, a stimulator of steroidogenesis. Informed from previous studies (see PR001844), dansyl hydrazine and dansyl chloride (DnHz and DnCl respectively) were employed via an in-house method to enhance detection of specific sub metabolomes (e.g., estrogens and other steroids) in supernatant derived from the described cells. Derivatized samples were analyzed using a Thermo Scientific Q Exactive HF-X Mass Spectrometer coupled to a Thermo Vanquish Duo UHPLC Systems, equipped with an HES-II ionization source. The analysis uses a RP positive method optimized for derivatized samples. By comparing the steroid profiles of these samples, phenotypic differences can be explained at a molecular level. This is particularly useful for non-transcriptional factors that can otherwise be difficult to characterize with transcriptomics approaches. 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. 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
The Jackson Laboratory for Genomic Medicine
Last NameChi
First NameYuanye
Address10 Discovery Dr, Farmington, CT
Emailyuanye.chi@jax.org
Phone3395456866
Submit Date2025-05-13
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-06-09
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:SU004089
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Sample source Harvest
SA452392Pool_12C13C_DnCl_5_SZ_12042024_56Pool_12C13C Supernatant
SA452393Pool_12C13C_DnHz_2_SZ_12062024_20Pool_12C13C Supernatant
SA452394Pool_12C13C_DnHz_4_SZ_12062024_44Pool_12C13C Supernatant
SA452395Pool_12C13C_DnHz_5_SZ_12062024_56Pool_12C13C Supernatant
SA452396Pool_12C13C_DnHz_6_SZ_12062024_68Pool_12C13C Supernatant
SA452397Pool_12C13C_DnCl_2_SZ_12042024_20Pool_12C13C Supernatant
SA452398Pool_12C13C_DnCl_3_SZ_12042024_32Pool_12C13C Supernatant
SA452399Pool_12C13C_DnHz_1_SZ_12062024_07Pool_12C13C Supernatant
SA452400Pool_12C13C_DnHz_7_SZ_12062024_80Pool_12C13C Supernatant
SA452401Pool_12C13C_DnHz_8_SZ_12062024_92Pool_12C13C Supernatant
SA452402Pool_12C13C_DnHz_3_SZ_12062024_32Pool_12C13C Supernatant
SA452403Pool_12C13C_DnHz_9_SZ_12062024_102Pool_12C13C Supernatant
SA452404Pool_12C13C_DnCl_4_SZ_12042024_44Pool_12C13C Supernatant
SA452405Pool_12C13C_DnCl_9_SZ_12042024_102Pool_12C13C Supernatant
SA452406Pool_12C13C_DnCl_8_SZ_12042024_92Pool_12C13C Supernatant
SA452407Pool_12C13C_DnCl_1_SZ_12042024_07Pool_12C13C Supernatant
SA452408Pool_12C13C_DnCl_7_SZ_12042024_80Pool_12C13C Supernatant
SA452409Pool_12C13C_DnCl_6_SZ_12042024_68Pool_12C13C Supernatant
SA452410Pool_12C_DnHz_1_SZ_12062024_06Pool_12C Supernatant
SA452411Pool_12C_DnCl_9_SZ_12042024_101Pool_12C Supernatant
SA452412Pool_12C_DnCl_8_SZ_12042024_91Pool_12C Supernatant
SA452413Pool_12C_DnCl_3_SZ_12042024_31Pool_12C Supernatant
SA452414Pool_12C_DnCl_7_SZ_12042024_79Pool_12C Supernatant
SA452415Pool_12C_DnHz_2_SZ_12062024_19Pool_12C Supernatant
SA452416Pool_12C_DnCl_6_SZ_12042024_67Pool_12C Supernatant
SA452417Pool_12C_DnCl_4_SZ_12042024_43Pool_12C Supernatant
SA452418Pool_12C_DnHz_3_SZ_12062024_31Pool_12C Supernatant
SA452419Pool_12C_DnHz_4_SZ_12062024_43Pool_12C Supernatant
SA452420Pool_12C_DnHz_8_SZ_12062024_91Pool_12C Supernatant
SA452421Pool_12C_DnCl_1_SZ_12042024_06Pool_12C Supernatant
SA452422Pool_12C_DnHz_9_SZ_12062024_101Pool_12C Supernatant
SA452423Pool_12C_DnHz_5_SZ_12062024_55Pool_12C Supernatant
SA452424Pool_12C_DnCl_5_SZ_12042024_55Pool_12C Supernatant
SA452425Pool_12C_DnHz_7_SZ_12062024_79Pool_12C Supernatant
SA452426Pool_12C_DnCl_2_SZ_12042024_19Pool_12C Supernatant
SA452427Pool_12C_DnHz_6_SZ_12062024_67Pool_12C Supernatant
SA452428Pool_no_DnCl_1_12042024_04Pooled_Underivatized Supernatant
SA452429Pool_no_DnHz_2_SZ_12062024_105Pooled_Underivatized Supernatant
SA452430Pool_no_DnHz_1_12062024_04Pooled_Underivatized Supernatant
SA452431Pool_no_DnCl_2_SZ_12042024_105Pooled_Underivatized Supernatant
SA452432Process_Blank_12C_DnCl_2_SZ_12042024_107Process_Blank Supernatant
SA452433Process_Blank_12C_DnCl_1_SZ_12042024_02Process_Blank Supernatant
SA452434Process_Blank_12C13C_DnHz_2_SZ_12062024_106Process_Blank Supernatant
SA452435Process_Blank_12C_DnHz_2_SZ_12062024_107Process_Blank Supernatant
SA452436Process_Blank_12C_DnHz_1_SZ_12062024_02Process_Blank Supernatant
SA452437Process_Blank_12C13C_DnHz_SZ_12062024_03Process_Blank Supernatant
SA452438Process_Blank_12C13C_DnCl_SZ_12042024_03Process_Blank Supernatant
SA452439Process_Blank_12C13C_DnCl_2_SZ_12042024_106Process_Blank Supernatant
SA452440Qstd_1_SZ_12062024_08Qstd Supernatant
SA452441Qstd_2_SZ_12062024_103Qstd Supernatant
SA452442Qstd_2_SZ_12042024_103Qstd Supernatant
SA452443Qstd_1_SZ_12042024_08Qstd Supernatant
SA452444Solvent_Blank_2_SZ_12042024_108Solvent_Blank Supernatant
SA452445Solvent_Blank_2_SZ_12062024_108Solvent_Blank Supernatant
SA452446Solvent_Blank_1_SZ_12042024_01Solvent_Blank Supernatant
SA452447Solvent_Blank_1_SZ_12062024_01Solvent_Blank Supernatant
SA452448Standard_12C_DnCl_1_SZ_12042024_05Standard_12C Supernatant
SA452449Standard_12C_DnHz_2_SZ_12062024_104Standard_12C Supernatant
SA452450Standard_12C_DnCl_2_SZ_12042024_104Standard_12C Supernatant
SA452451Standard_12C_DnHz_1_SZ_12062024_05Standard_12C Supernatant
SA452452STS_PTC_C12_Basal_R1_12C_DnHz_SZ_12062024_58Stem Cells Culture Supernatant
SA452453STS_KO_A02_Basal_R1_12C_DnHz_SZ_12062024_53Stem Cells Culture Supernatant
SA452454STS_CE_C05_DHEAS_R1_12C_DnHz_SZ_12062024_54Stem Cells Culture Supernatant
SA452455STS_PTC_D10_DHEAS_R2_12C_DnCl_SZ_12042024_24Stem Cells Culture Supernatant
SA452456STS_PTC_F10_Basal_R1_12C_DnCl_SZ_12042024_23Stem Cells Culture Supernatant
SA452457STS_CE_B08_DHEAS_R2_12C_DnHz_SZ_12062024_57Stem Cells Culture Supernatant
SA452458STS_KO_A01_DHEAS_R1_12C_DnHz_SZ_12062024_61Stem Cells Culture Supernatant
SA452459STS_PTC_D10_DHEAS_R3_12C_DnHz_SZ_12062024_59Stem Cells Culture Supernatant
SA452460HSD3B1_PTC_C07_DHEAS_R3_12C_DnHz_SZ_12062024_60Stem Cells Culture Supernatant
SA452461STS_KO_B03_Basal_R2_12C_DnHz_SZ_12062024_51Stem Cells Culture Supernatant
SA452462HSD3B1_PTC_C07_Basal_R2_12C_DnHz_SZ_12062024_62Stem Cells Culture Supernatant
SA452463STS_CE_A06_Basal_R2_12C_DnHz_SZ_12062024_63Stem Cells Culture Supernatant
SA452464STS_PTC_D10_Basal_R2_12C_DnHz_SZ_12062024_64Stem Cells Culture Supernatant
SA452465WT_DHEAS_3_12C_DnHz_SZ_12062024_65Stem Cells Culture Supernatant
SA452466STS_CE_B08_Basal_R2_12C_DnHz_SZ_12062024_66Stem Cells Culture Supernatant
SA452467WT_Basal_3_12C_DnHz_SZ_12062024_52Stem Cells Culture Supernatant
SA452468STS_CE_A06_DHEAS_R3_12C_DnHz_SZ_12062024_49Stem Cells Culture Supernatant
SA452469STS_KO_A02_DHEAS_R2_12C_DnHz_SZ_12062024_50Stem Cells Culture Supernatant
SA452470STS_KO_A01_Basal_R2_12C_DnHz_SZ_12062024_40Stem Cells Culture Supernatant
SA452471STS_CE_A06_DHEAS_R2_12C_DnHz_SZ_12062024_33Stem Cells Culture Supernatant
SA452472STS_KO_A01_DHEAS_R2_12C_DnHz_SZ_12062024_34Stem Cells Culture Supernatant
SA452473STS_PTC_C12_Basal_R3_12C_DnHz_SZ_12062024_35Stem Cells Culture Supernatant
SA452474STS_PTC_F10_Basal_R1_12C_DnHz_SZ_12062024_36Stem Cells Culture Supernatant
SA452475STS_CE_C05_DHEAS_R3_12C_DnHz_SZ_12062024_37Stem Cells Culture Supernatant
SA452476HSD3B1_PTC_D03_DHEAS_R3_12C_DnHz_SZ_12062024_38Stem Cells Culture Supernatant
SA452477STS_PTC_C12_DHEAS_R2_12C_DnHz_SZ_12062024_39Stem Cells Culture Supernatant
SA452478HSD3B1_PTC_C12_DHEAS_R1_12C_DnHz_SZ_12062024_41Stem Cells Culture Supernatant
SA452479STS_CE_B08_DHEAS_R2_12C_DnCl_SZ_12042024_21Stem Cells Culture Supernatant
SA452480STS_PTC_F10_Basal_R3_12C_DnHz_SZ_12062024_42Stem Cells Culture Supernatant
SA452481STS_CE_C05_DHEAS_R2_12C_DnCl_SZ_12042024_26Stem Cells Culture Supernatant
SA452482STS_KO_B03_Basal_R1_12C_DnCl_SZ_12042024_25Stem Cells Culture Supernatant
SA452483STS_KO_B03_DHEAS_R2_12C_DnHz_SZ_12062024_45Stem Cells Culture Supernatant
SA452484STS_CE_C05_Basal_R3_12C_DnHz_SZ_12062024_46Stem Cells Culture Supernatant
SA452485HSD3B1_PTC_D03_Basal_R3_12C_DnHz_SZ_12062024_47Stem Cells Culture Supernatant
SA452486HSD3B1_PTC_C12_Basal_R3_12C_DnHz_SZ_12062024_48Stem Cells Culture Supernatant
SA452487STS_PTC_F10_DHEAS_R3_12C_DnCl_SZ_12042024_22Stem Cells Culture Supernatant
SA452488HSD3B1_PTC_D03_DHEAS_R1_12C_DnHz_SZ_12062024_70Stem Cells Culture Supernatant
SA452489STS_PTC_F10_DHEAS_R3_12C_DnHz_SZ_12062024_69Stem Cells Culture Supernatant
SA452490HSD3B1_PTC_D03_DHEAS_R2_12C_DnHz_SZ_12062024_98Stem Cells Culture Supernatant
SA452491STS_KO_A01_DHEAS_R2_12C_DnCl_SZ_12042024_16Stem Cells Culture Supernatant
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Collection:

Collection ID:CO004082
Collection Summary:For the media collection, 500 µL of media was directly aspirated into 1.5 mL Eppendorf tube from each well and flash frozen with liquid nitrogen, stored immediately at -80°C.
Sample Type:iPSC cells

Treatment:

Treatment ID:TR004098
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:SP004095
Sampleprep Summary:See from protocol file.
Sampleprep Protocol Filename:DnCl_Protocol_one_phase_extraction_SZ_05132025.pdf
DnHz_Protocol_one_phase_extraction_SZ_05132025.pdf
OnePhaseSupernatant_Protocol_SZ_05132025.pdf
OnePhaseCellPellet_Protocol_SZ_05132025.pdf

Chromatography:

Chromatography ID:CH004935
Chromatography Summary:See protocol file
Methods Filename:DnCl_DnHZ_LC_MS_Protocol_SZ_05132025.pdf
Instrument Name:Thermo Vanquish Duo UHPLC
Column Name:Waters ACQUITY UPLC CSH C18 (100 x 2.1 mm, 1.7 µm)
Column Temperature:45°C
Flow Gradient:0.0min: 100%B, 3.0min: 100%B, 16.0min: 65%B, 18.0min: 100%B, 21.0min: 100%B, 21.5min: 0%B, 26.0min: 0%B.
Flow Rate:0.4 mL/min
Solvent A:95% water/5% acetonitrile; 0.1% Formic acid
Solvent B:100% acetonitrile; 0.1% Formic acid (v/v)
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN006495
Analysis Type:MS
Analysis Protocol File:DnCl_DnHZ_LC_MS_Protocol_SZ_05132025.pdf
Chromatography ID:CH004935
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST003952_AN006495_Results.txt
Units:peak intensity
  
Analysis ID:AN006496
Analysis Type:MS
Analysis Protocol File:DnCl_DnHZ_LC_MS_Protocol_SZ_05132025.pdf
Chromatography ID:CH004935
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST003952_AN006496_Results.txt
Units:peak intensity
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