Summary of Study ST002965

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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST002965
Study TitleComprehensive Untargeted LC-MS Metabolomics Analysis of CYP19A1/PRLR/PTN Knockout iPSCs - Part 2
Study SummaryHuman induced pluripotent stem cells (hIPSCs) are a key tool for biomedical research. In this study, human induced pluripotent stem cells of the KOLF2.1 lineage were generated with null allele mutations for CYP19A1, PRLR, and PTN. 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 supernatant 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 Date2023-10-31
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-05-14
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:SU003078
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Cell Line Differentiation Media Additives
SA322740Media_20_HILICposcyp19a1 KO differentiated basal -
SA322741Media_20_HILICnegcyp19a1 KO differentiated basal -
SA322742Media_19_Rpposcyp19a1 KO differentiated basal -
SA322743Media_19_HILICposcyp19a1 KO differentiated basal -
SA322744Media_19_Rpnegcyp19a1 KO differentiated basal -
SA322745Media_20_Rpnegcyp19a1 KO differentiated basal -
SA322746Media_20_Rpposcyp19a1 KO differentiated basal -
SA322747Media_49_HILICnegcyp19a1 KO differentiated basal -
SA322748Media_21_Rpposcyp19a1 KO differentiated basal -
SA322749Media_21_Rpnegcyp19a1 KO differentiated basal -
SA322750Media_21_HILICposcyp19a1 KO differentiated basal -
SA322751Media_21_HILICnegcyp19a1 KO differentiated basal -
SA322752Media_19_HILICnegcyp19a1 KO differentiated basal -
SA322753Media_50_HILICnegcyp19a1 KO differentiated basal -
SA322754Media_49_Rpposcyp19a1 KO differentiated basal -
SA322755Media_51_Rpposcyp19a1 KO differentiated basal -
SA322756Media_50_Rpposcyp19a1 KO differentiated basal -
SA322757Media_50_Rpnegcyp19a1 KO differentiated basal -
SA322758Media_49_Rpnegcyp19a1 KO differentiated basal -
SA322759Media_49_HILICposcyp19a1 KO differentiated basal -
SA322760Media_51_HILICposcyp19a1 KO differentiated basal -
SA322761Media_50_HILICposcyp19a1 KO differentiated basal -
SA322762Media_51_Rpnegcyp19a1 KO differentiated basal -
SA322763Media_51_HILICnegcyp19a1 KO differentiated basal -
SA322764Media_22_Rpposcyp19a1 KO differentiated basal dheas
SA322765Media_22_Rpnegcyp19a1 KO differentiated basal dheas
SA322766Media_23_HILICposcyp19a1 KO differentiated basal dheas
SA322767Media_24_Rpposcyp19a1 KO differentiated basal dheas
SA322768Media_24_HILICposcyp19a1 KO differentiated basal dheas
SA322769Media_24_HILICnegcyp19a1 KO differentiated basal dheas
SA322770Media_23_Rpposcyp19a1 KO differentiated basal dheas
SA322771Media_23_Rpnegcyp19a1 KO differentiated basal dheas
SA322772Media_24_Rpnegcyp19a1 KO differentiated basal dheas
SA322773Media_23_HILICnegcyp19a1 KO differentiated basal dheas
SA322774Media_22_HILICnegcyp19a1 KO differentiated basal dheas
SA322775Media_22_HILICposcyp19a1 KO differentiated basal dheas
SA322776Media_54_HILICposcyp19a1 KO differentiated complex -
SA322777Media_54_Rpnegcyp19a1 KO differentiated complex -
SA322778Media_54_Rpposcyp19a1 KO differentiated complex -
SA322779Media_54_HILICnegcyp19a1 KO differentiated complex -
SA322780Media_52_HILICnegcyp19a1 KO differentiated complex -
SA322781Media_53_Rpposcyp19a1 KO differentiated complex -
SA322782Media_52_Rpnegcyp19a1 KO differentiated complex -
SA322783Media_52_HILICposcyp19a1 KO differentiated complex -
SA322784Media_53_HILICnegcyp19a1 KO differentiated complex -
SA322785Media_52_Rpposcyp19a1 KO differentiated complex -
SA322786Media_53_Rpnegcyp19a1 KO differentiated complex -
SA322787Media_53_HILICposcyp19a1 KO differentiated complex -
SA322788Media_7_HILICnegcyp19a1 KO ipsc basal -
SA322789Media_7_Rpnegcyp19a1 KO ipsc basal -
SA322790Media_7_HILICposcyp19a1 KO ipsc basal -
SA322791Media_8_HILICnegcyp19a1 KO ipsc basal -
SA322792Media_7_Rpposcyp19a1 KO ipsc basal -
SA322793Media_8_Rpposcyp19a1 KO ipsc basal -
SA322794Media_9_HILICnegcyp19a1 KO ipsc basal -
SA322795Media_9_Rpnegcyp19a1 KO ipsc basal -
SA322796Media_9_Rpposcyp19a1 KO ipsc basal -
SA322797Media_8_Rpnegcyp19a1 KO ipsc basal -
SA322798Media_9_HILICposcyp19a1 KO ipsc basal -
SA322799Media_8_HILICposcyp19a1 KO ipsc basal -
SA322800Media_12_HILICposcyp19a1 KO ipsc basal dheas
SA322801Media_11_HILICnegcyp19a1 KO ipsc basal dheas
SA322802Media_12_Rpposcyp19a1 KO ipsc basal dheas
SA322803Media_12_HILICnegcyp19a1 KO ipsc basal dheas
SA322804Media_10_HILICnegcyp19a1 KO ipsc basal dheas
SA322805Media_12_Rpnegcyp19a1 KO ipsc basal dheas
SA322806Media_11_Rpposcyp19a1 KO ipsc basal dheas
SA322807Media_11_Rpnegcyp19a1 KO ipsc basal dheas
SA322808Media_10_Rpposcyp19a1 KO ipsc basal dheas
SA322809Media_11_HILICposcyp19a1 KO ipsc basal dheas
SA322810Media_10_Rpnegcyp19a1 KO ipsc basal dheas
SA322811Media_10_HILICposcyp19a1 KO ipsc basal dheas
SA322704Pool_QC_Media_RPpos_2- - - -
SA322705Pool_QC_Media_RPpos_1- - - -
SA322706Pool_QC_Media_RPneg_DDA- - - -
SA322707Pool_QC_Media_RPpos_DDA- - - -
SA322708Qstd_HILICneg_1- - - -
SA322709Qstd_RPneg_1- - - -
SA322710Qstd_HILICpos_2- - - -
SA322711Qstd_HILICpos_1- - - -
SA322712Qstd_HILICneg_2- - - -
SA322713Pool_QC_Media_RPneg_3- - - -
SA322714Pool_QC_Media_RPneg_2- - - -
SA322715Pool_QC_Media_HILICneg_DDA- - - -
SA322716Pool_QC_Media_HILICneg_3- - - -
SA322717Pool_QC_Media_HILICneg_2- - - -
SA322718Pool_QC_Media_HILICneg_1- - - -
SA322719Pool_QC_Media_HILICpos_1- - - -
SA322720Pool_QC_Media_HILICpos_2- - - -
SA322721Pool_QC_Media_RPneg_1- - - -
SA322722Pool_QC_Media_HILICpos_DDA- - - -
SA322723Pool_QC_Media_HILICpos_3- - - -
SA322724Blank_HILICneg_1- - - -
SA322725Pool_QC_Media_RPpos_3- - - -
SA322726Blank_IS_RPpos_2- - - -
SA322727Blank_IS_RPpos_1- - - -
SA322728Blank_RPneg_1- - - -
SA322729Blank_RPpos_1- - - -
SA322730Qstd_RPpos_2- - - -
SA322731Blank_IS_RPneg_2- - - -
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 252

Collection:

Collection ID:CO003071
Collection Summary:Remove the supernatant and flash freeze with liquid nitrogen and store immediately at -80C.
Sample Type:iPSC cells

Treatment:

Treatment ID:TR003087
Treatment Summary:Firstly seed 50,000 cells of the wild type and knockout lines per well in a 6 well plate in triplicate and incubate at 37C, after 24h add trophectoderm media (TE) containing the growth factors BMP4 and SU5402 (day 0). Two days after (day 2), add the same media containing SU5402, BMP4 and A-83 and repeat this again after 2 days (day 4). Finally, after another 2 days (day 6) remove the differentiation media and add basal or complex media to the cells and incubate for 24h at 37C.

Sample Preparation:

Sampleprep ID:SP003084
Sampleprep Summary:See from protocol file.
Sampleprep Protocol Filename:TwoPhaseSupernatantExtract_Protocol_10_10_23_v3.pdf

Chromatography:

Chromatography ID:CH003675
Methods Filename:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore HILIC (100 x 2.1mm,2.6um)
Column Temperature:45
Flow Gradient:From 0 to 0.20 minutes, B is 0% with a flow rate of 550 µL/min; it jumps to 98% by 8.75 minutes (still at 550 µL/min) and remains until 10 minutes; at 15 minutes, B returns to 0% but the flow drops to 100 µL/min, then rises back to 550 µL/min by 17 minutes, staying consistent until 20 minutes.
Flow Rate:550->100->550µL/min
Solvent A:95% ACN/water (10 mM ammonium acetate, 0.1% acetic acid)
Solvent B:50% ACN/water (10 mM ammonium acetate, 0.1% acetic acid)
Chromatography Type:HILIC
  
Chromatography ID:CH003676
Methods Filename:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Instrument Name:Thermo Vanquish
Column Name:Hypersil GOLD C18 (50 x 2.1mm, 3um)
Column Temperature:45
Flow Gradient:From 0 to 0.01 minutes, B is 15% at a flow rate of 400 µL/min; by 2.01 minutes, it's 30%, reaching 48% at 2.51 minutes, then 82% by 11 minutes, and it sharply rises to 99% at 11.50 minutes holding until 16.50 minutes when it peaks at 100%; from 17.50 to 20 minutes, it drops back to 15%, with the flow rate consistently maintained at 400 µL/min throughout.
Flow Rate:400µL/min
Solvent A:60% ACN/water (10 mM ammonium formate, 0.1% formic acid)
Solvent B:90% 2-propanol/ACN (10 mM ammonium formate, 0.1% formic acid)
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN004869
Analysis Type:MS
Analysis Protocol File:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Chromatography ID:CH003675
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST002965_AN004869_Results.txt
Units:peak intensity
  
Analysis ID:AN004870
Analysis Type:MS
Analysis Protocol File:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Chromatography ID:CH003675
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST002965_AN004870_Results.txt
Units:peak intensity
  
Analysis ID:AN004871
Analysis Type:MS
Analysis Protocol File:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Chromatography ID:CH003676
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST002965_AN004871_Results.txt
Units:peak intensity
  
Analysis ID:AN004872
Analysis Type:MS
Analysis Protocol File:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Chromatography ID:CH003676
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST002965_AN004872_Results.txt
Units:peak intensity
  logo