Summary of Study ST002964

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 IDST002964
Study TitleComprehensive Untargeted LC-MS Metabolomics Analysis of CYP19A1/PRLR/PTN Knockout iPSCs
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 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 Date2023-10-05
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:SU003077
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
SA322488Pellets_20_HILICposcyp19a1 KO differentiated basal -
SA322489Pellets_20_HILICnegcyp19a1 KO differentiated basal -
SA322490Pellets_19_Rpposcyp19a1 KO differentiated basal -
SA322491Pellets_19_HILICposcyp19a1 KO differentiated basal -
SA322492Pellets_19_Rpnegcyp19a1 KO differentiated basal -
SA322493Pellets_20_Rpnegcyp19a1 KO differentiated basal -
SA322494Pellets_20_Rpposcyp19a1 KO differentiated basal -
SA322495Pellets_49_HILICnegcyp19a1 KO differentiated basal -
SA322496Pellets_21_Rpposcyp19a1 KO differentiated basal -
SA322497Pellets_21_Rpnegcyp19a1 KO differentiated basal -
SA322498Pellets_21_HILICposcyp19a1 KO differentiated basal -
SA322499Pellets_21_HILICnegcyp19a1 KO differentiated basal -
SA322500Pellets_19_HILICnegcyp19a1 KO differentiated basal -
SA322501Pellets_50_HILICnegcyp19a1 KO differentiated basal -
SA322502Pellets_49_Rpposcyp19a1 KO differentiated basal -
SA322503Pellets_51_Rpposcyp19a1 KO differentiated basal -
SA322504Pellets_50_Rpposcyp19a1 KO differentiated basal -
SA322505Pellets_50_Rpnegcyp19a1 KO differentiated basal -
SA322506Pellets_49_Rpnegcyp19a1 KO differentiated basal -
SA322507Pellets_49_HILICposcyp19a1 KO differentiated basal -
SA322508Pellets_51_HILICposcyp19a1 KO differentiated basal -
SA322509Pellets_50_HILICposcyp19a1 KO differentiated basal -
SA322510Pellets_51_Rpnegcyp19a1 KO differentiated basal -
SA322511Pellets_51_HILICnegcyp19a1 KO differentiated basal -
SA322512Pellets_22_Rpposcyp19a1 KO differentiated basal dheas
SA322513Pellets_22_Rpnegcyp19a1 KO differentiated basal dheas
SA322514Pellets_23_HILICposcyp19a1 KO differentiated basal dheas
SA322515Pellets_24_Rpposcyp19a1 KO differentiated basal dheas
SA322516Pellets_24_HILICposcyp19a1 KO differentiated basal dheas
SA322517Pellets_24_HILICnegcyp19a1 KO differentiated basal dheas
SA322518Pellets_23_Rpposcyp19a1 KO differentiated basal dheas
SA322519Pellets_23_Rpnegcyp19a1 KO differentiated basal dheas
SA322520Pellets_24_Rpnegcyp19a1 KO differentiated basal dheas
SA322521Pellets_23_HILICnegcyp19a1 KO differentiated basal dheas
SA322522Pellets_22_HILICnegcyp19a1 KO differentiated basal dheas
SA322523Pellets_22_HILICposcyp19a1 KO differentiated basal dheas
SA322524Pellets_54_HILICposcyp19a1 KO differentiated complex -
SA322525Pellets_54_Rpnegcyp19a1 KO differentiated complex -
SA322526Pellets_54_Rpposcyp19a1 KO differentiated complex -
SA322527Pellets_54_HILICnegcyp19a1 KO differentiated complex -
SA322528Pellets_52_HILICnegcyp19a1 KO differentiated complex -
SA322529Pellets_53_Rpposcyp19a1 KO differentiated complex -
SA322530Pellets_52_Rpnegcyp19a1 KO differentiated complex -
SA322531Pellets_52_HILICposcyp19a1 KO differentiated complex -
SA322532Pellets_53_HILICnegcyp19a1 KO differentiated complex -
SA322533Pellets_52_Rpposcyp19a1 KO differentiated complex -
SA322534Pellets_53_Rpnegcyp19a1 KO differentiated complex -
SA322535Pellets_53_HILICposcyp19a1 KO differentiated complex -
SA322536Pellets_7_HILICnegcyp19a1 KO ipsc basal -
SA322537Pellets_7_Rpnegcyp19a1 KO ipsc basal -
SA322538Pellets_7_HILICposcyp19a1 KO ipsc basal -
SA322539Pellets_8_HILICnegcyp19a1 KO ipsc basal -
SA322540Pellets_7_Rpposcyp19a1 KO ipsc basal -
SA322541Pellets_8_Rpposcyp19a1 KO ipsc basal -
SA322542Pellets_9_HILICnegcyp19a1 KO ipsc basal -
SA322543Pellets_9_Rpnegcyp19a1 KO ipsc basal -
SA322544Pellets_9_Rpposcyp19a1 KO ipsc basal -
SA322545Pellets_8_Rpnegcyp19a1 KO ipsc basal -
SA322546Pellets_9_HILICposcyp19a1 KO ipsc basal -
SA322547Pellets_8_HILICposcyp19a1 KO ipsc basal -
SA322548Pellets_12_HILICposcyp19a1 KO ipsc basal dheas
SA322549Pellets_11_HILICnegcyp19a1 KO ipsc basal dheas
SA322550Pellets_12_Rpposcyp19a1 KO ipsc basal dheas
SA322551Pellets_12_HILICnegcyp19a1 KO ipsc basal dheas
SA322552Pellets_10_HILICnegcyp19a1 KO ipsc basal dheas
SA322553Pellets_12_Rpnegcyp19a1 KO ipsc basal dheas
SA322554Pellets_11_Rpposcyp19a1 KO ipsc basal dheas
SA322555Pellets_11_Rpnegcyp19a1 KO ipsc basal dheas
SA322556Pellets_10_Rpposcyp19a1 KO ipsc basal dheas
SA322557Pellets_11_HILICposcyp19a1 KO ipsc basal dheas
SA322558Pellets_10_Rpnegcyp19a1 KO ipsc basal dheas
SA322559Pellets_10_HILICposcyp19a1 KO ipsc basal dheas
SA322452Pool_QC_Pellets_RPpos_2- - - -
SA322453Pool_QC_Pellets_RPpos_1- - - -
SA322454Pool_QC_Pellets_RPneg_DDA- - - -
SA322455Pool_QC_Pellets_RPpos_DDA- - - -
SA322456Qstd_HILICneg_1- - - -
SA322457Qstd_RPneg_1- - - -
SA322458Qstd_HILICpos_2- - - -
SA322459Qstd_HILICpos_1- - - -
SA322460Qstd_HILICneg_2- - - -
SA322461Pool_QC_Pellets_RPneg_3- - - -
SA322462Pool_QC_Pellets_RPneg_2- - - -
SA322463Pool_QC_Pellets_HILICneg_DDA- - - -
SA322464Pool_QC_Pellets_HILICneg_3- - - -
SA322465Pool_QC_Pellets_HILICneg_2- - - -
SA322466Pool_QC_Pellets_HILICneg_1- - - -
SA322467Pool_QC_Pellets_HILICpos_1- - - -
SA322468Pool_QC_Pellets_HILICpos_2- - - -
SA322469Pool_QC_Pellets_RPneg_1- - - -
SA322470Pool_QC_Pellets_HILICpos_DDA- - - -
SA322471Pool_QC_Pellets_HILICpos_3- - - -
SA322472Blank_HILICneg_1- - - -
SA322473Pool_QC_Pellets_RPpos_3- - - -
SA322474Blank_IS_RPpos_2- - - -
SA322475Blank_IS_RPpos_1- - - -
SA322476Blank_RPneg_1- - - -
SA322477Blank_RPpos_1- - - -
SA322478Qstd_RPpos_2- - - -
SA322479Blank_IS_RPneg_2- - - -
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Collection:

Collection ID:CO003070
Collection Summary:Remove the supernatant and flash freeze with liquid nitrogen and store immediately at -80C. Wash the wells once with PBS and then add accutase and incubate at 37C for 7min. Aspirate the accutase and add stemflex media and with a cell lifter scrape off the cells from the bottom of the well. Transfer the cell lysate to an Eppendorf tube and wash twice with PBS by centrifuging at 300g for 5min. Finally remove the PBS and flash freeze the pellet in liquid nitrogen and store immediately at -80C.
Sample Type:iPSC cells

Treatment:

Treatment ID:TR003086
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:SP003083
Sampleprep Summary:See from protocol file.
Sampleprep Protocol Filename:TwoPhaseCellExtract_Protocol_10_10_23_v3.pdf

Chromatography:

Chromatography ID:CH003673
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:CH003674
Methods Filename:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Instrument Name:Thermo Vanquish
Column Name:Hypersil GOLD (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:AN004865
Analysis Type:MS
Analysis Protocol File:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Chromatography ID:CH003673
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST002964_AN004865_Results.txt
Units:peak intensity
  
Analysis ID:AN004866
Analysis Type:MS
Analysis Protocol File:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Chromatography ID:CH003673
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST002964_AN004866_Results.txt
Units:peak intensity
  
Analysis ID:AN004867
Analysis Type:MS
Analysis Protocol File:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Chromatography ID:CH003674
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST002964_AN004867_Results.txt
Units:peak intensity
  
Analysis ID:AN004868
Analysis Type:MS
Analysis Protocol File:Regular_LC_MS_Protocol_10_25_23_v2.pdf
Chromatography ID:CH003674
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST002964_AN004868_Results.txt
Units:peak intensity
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