Summary of Study ST002284
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 PR001464. The data can be accessed directly via it's Project DOI: 10.21228/M8GT5D 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.
| Study ID | ST002284 |
| Study Title | Genetically defined human GBM organoids reveal principles of GBM development and actionable targets |
| Study Summary | Recent advances in glioblastoma (GBM) studies provide a comprehensive catalog of its genetic aberrations and cellular heterogeneity. However, a solid understanding of genotype-based analysis of cancer pathway dependency and actionable target identification is required to transform GBM treatment into a personalized era. Here, we generated a spectrum of mutant iPSCs harboring frequent GBM mutations with CRISPR/Cas9 and profiled the organoids (LEGO: Laboratory Engineered Glioblastoma Organoid) derived from these iPSCs temporally on transcriptome, methylome, metabolome, lipidome, proteome, and phospho-proteome levels. We found that LEGOs form brain tumors in vivo and recapitulate critical features of human GBM. The multi-omics analysis discovered essential milestones driven by genetic heterogeneity during GBM progressions, such as lineage alteration, methylome rewriting, and metabolome/lipidome reprogramming, in concordance with altered pathway activity and drug response. This study provides a tool and research path to realizing genome-based personalized GBM therapy using novel advanced models. |
| Institute | DKFZ |
| Department | Molecular Neurogenetics |
| Laboratory | Molecular Neurogenetics |
| Last Name | Wang |
| First Name | Changwen |
| Address | Im Neuenheimer Feld 581 |
| c.wang@dkfz-heidelberg.de | |
| Phone | +49 6221 42 3455 |
| Submit Date | 2022-09-17 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-01-26 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Age | Extracted Sample |
|---|---|---|---|---|
| SA218667 | LS21_049_Med_Lip_S22_1m_woCells_2 | "NA, blank medium control" | "NA, same batch medium as 1-month-old" | Culture medium |
| SA218668 | LS21_049_Med_Lip_S23_1m_woCells_3 | "NA, blank medium control" | "NA, same batch medium as 1-month-old" | Culture medium |
| SA218669 | LS21_049_Med_Lip_S24_1m_woCells_4 | "NA, blank medium control" | "NA, same batch medium as 1-month-old" | Culture medium |
| SA218670 | LS21_049_Med_Lip_S21_1m_woCells_1 | "NA, blank medium control" | "NA, same batch medium as 1-month-old" | Culture medium |
| SA218671 | LS21_049_Med_S21_1m_woCells_1 | "NA, blank medium control" | "NA, same batch medium as 1-month-old" | Culture medium |
| SA218672 | LS21_049_Med_S22_1m_woCells_2 | "NA, blank medium control" | "NA, same batch medium as 1-month-old" | Culture medium |
| SA218673 | LS21_049_Med_S25_1m_woCells_5 | "NA, blank medium control" | "NA, same batch medium as 1-month-old" | Culture medium |
| SA218674 | LS21_049_Med_S24_1m_woCells_4 | "NA, blank medium control" | "NA, same batch medium as 1-month-old" | Culture medium |
| SA218675 | LS21_049_Med_S23_1m_woCells_3 | "NA, blank medium control" | "NA, same batch medium as 1-month-old" | Culture medium |
| SA218676 | LS21_049_Med_Lip_S25_1m_woCells_5 | "NA, blank medium control" | "NA, same batch medium as 1-month-old" | Culture medium |
| SA218677 | LS21_049_Med_Lip_S46_4m_woCells_1 | "NA, blank medium control" | "NA, same batch medium as 4-month-old" | Culture medium |
| SA218678 | LS21_049_Med_S46_4m_woCells_1 | "NA, blank medium control" | "NA, same batch medium as 4-month-old" | Culture medium |
| SA218679 | LS21_049_Med_Lip_S47_4m_woCells_2 | "NA, blank medium control" | "NA, same batch medium as 4-month-old" | Culture medium |
| SA218680 | LS21_049_Med_S50_4m_woCells_5 | "NA, blank medium control" | "NA, same batch medium as 4-month-old" | Culture medium |
| SA218681 | LS21_049_Med_Lip_S50_4m_woCells_5 | "NA, blank medium control" | "NA, same batch medium as 4-month-old" | Culture medium |
| SA218682 | LS21_049_Med_Lip_S49_4m_woCells_4 | "NA, blank medium control" | "NA, same batch medium as 4-month-old" | Culture medium |
| SA218683 | LS21_049_Med_Lip_S48_4m_woCells_3 | "NA, blank medium control" | "NA, same batch medium as 4-month-old" | Culture medium |
| SA218684 | LS21_049_Med_S47_4m_woCells_2 | "NA, blank medium control" | "NA, same batch medium as 4-month-old" | Culture medium |
| SA218685 | LS21_049_Med_S49_4m_woCells_4 | "NA, blank medium control" | "NA, same batch medium as 4-month-old" | Culture medium |
| SA218686 | LS21_049_Med_S48_4m_woCells_3 | "NA, blank medium control" | "NA, same batch medium as 4-month-old" | Culture medium |
| SA218727 | LS21_049_Med_S12_1m_PTCC_2 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Culture medium |
| SA218728 | LS21_049_Med_S13_1m_PTCC_3 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Culture medium |
| SA218729 | LS21_049_Med_Lip_S12_1m_PTCC_2 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Culture medium |
| SA218730 | LS21_049_Med_Lip_S13_1m_PTCC_3 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Culture medium |
| SA218731 | LS21_049_Med_Lip_S15_1m_PTCC_5 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Culture medium |
| SA218732 | LS21_049_Med_Lip_S14_1m_PTCC_4 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Culture medium |
| SA218733 | LS21_049_Med_S14_1m_PTCC_4 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Culture medium |
| SA218734 | LS21_049_Med_Lip_S11_1m_PTCC_1 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Culture medium |
| SA218735 | LS21_049_Med_S15_1m_PTCC_5 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Culture medium |
| SA218736 | LS21_049_Med_S11_1m_PTCC_1 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Culture medium |
| SA218737 | LS21_049_Org_S14_1m_PTCC_4 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Organoid |
| SA218738 | LS21_049_Org_S13_1m_PTCC_3 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Organoid |
| SA218739 | LS21_049_Org_S12_1m_PTCC_2 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Organoid |
| SA218740 | LS21_049_Org_S11_1m_PTCC_1 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Organoid |
| SA218741 | LS21_049_Org_S15_1m_PTCC_5 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Organoid |
| SA218742 | LS21_049_Lip_Org_S14_1m_PTCC_4 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Organoid |
| SA218743 | LS21_049_Lip_Org_S13_1m_PTCC_3 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Organoid |
| SA218744 | LS21_049_Lip_Org_S15_1m_PTCC_5 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Organoid |
| SA218745 | LS21_049_Lip_Org_S12_1m_PTCC_2 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Organoid |
| SA218746 | LS21_049_Lip_Org_S11_1m_PTCC_1 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 1-month-old | Organoid |
| SA218747 | LS21_049_Med_Lip_S37_4m_PTCC_2 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Culture medium |
| SA218748 | LS21_049_Med_Lip_S36_4m_PTCC_1 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Culture medium |
| SA218749 | LS21_049_Med_S36_4m_PTCC_1 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Culture medium |
| SA218750 | LS21_049_Med_S38_4m_PTCC_3 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Culture medium |
| SA218751 | LS21_049_Med_S37_4m_PTCC_2 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Culture medium |
| SA218752 | LS21_049_Med_Lip_S38_4m_PTCC_3 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Culture medium |
| SA218753 | LS21_049_Med_Lip_S40_4m_PTCC_5 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Culture medium |
| SA218754 | LS21_049_Med_S39_4m_PTCC_4 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Culture medium |
| SA218755 | LS21_049_Med_Lip_S39_4m_PTCC_4 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Culture medium |
| SA218756 | LS21_049_Med_S40_4m_PTCC_5 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Culture medium |
| SA218757 | LS21_049_Org_S35_4m_PTCC_5 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Organoid |
| SA218758 | LS21_049_Org_S33_4m_PTCC_3 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Organoid |
| SA218759 | LS21_049_Lip_Org_S32_4m_PTCC_2 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Organoid |
| SA218760 | LS21_049_Org_S34_4m_PTCC_4 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Organoid |
| SA218761 | LS21_049_Lip_Org_S34_4m_PTCC_4 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Organoid |
| SA218762 | LS21_049_Lip_Org_S33_4m_PTCC_3 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Organoid |
| SA218763 | LS21_049_Org_S32_4m_PTCC_2 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Organoid |
| SA218764 | LS21_049_Org_S31_4m_PTCC_1 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Organoid |
| SA218765 | LS21_049_Lip_Org_S35_4m_PTCC_5 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Organoid |
| SA218766 | LS21_049_Lip_Org_S31_4m_PTCC_1 | PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- | 4-month-old | Organoid |
| SA218767 | LS21_049_Med_Lip_S16_1m_PTN_1 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Culture medium |
| SA218768 | LS21_049_Med_Lip_S19_1m_PTN_4 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Culture medium |
| SA218769 | LS21_049_Med_Lip_S17_1m_PTN_2 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Culture medium |
| SA218770 | LS21_049_Med_Lip_S18_1m_PTN_3 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Culture medium |
| SA218771 | LS21_049_Med_S20_1m_PTN_5 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Culture medium |
| SA218772 | LS21_049_Med_S18_1m_PTN_3 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Culture medium |
| SA218773 | LS21_049_Med_S19_1m_PTN_4 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Culture medium |
| SA218774 | LS21_049_Med_Lip_S20_1m_PTN_5 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Culture medium |
| SA218775 | LS21_049_Med_S17_1m_PTN_2 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Culture medium |
| SA218776 | LS21_049_Med_S16_1m_PTN_1 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Culture medium |
| SA218777 | LS21_049_Org_S20_1m_PTN_5 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Organoid |
| SA218778 | LS21_049_Org_S19_1m_PTN_4 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Organoid |
| SA218779 | LS21_049_Org_S18_1m_PTN_3 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Organoid |
| SA218780 | LS21_049_Lip_Org_S18_1m_PTN_3 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Organoid |
| SA218781 | LS21_049_Org_S16_1m_PTN_1 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Organoid |
| SA218782 | LS21_049_Org_S17_1m_PTN_2 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Organoid |
| SA218783 | LS21_049_Lip_Org_S17_1m_PTN_2 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Organoid |
| SA218784 | LS21_049_Lip_Org_S16_1m_PTN_1 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Organoid |
| SA218785 | LS21_049_Lip_Org_S19_1m_PTN_4 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Organoid |
| SA218786 | LS21_049_Lip_Org_S20_1m_PTN_5 | PTN; PTEN-/-; TP53-/-; NF1-/- | 1-month-old | Organoid |
| SA218787 | LS21_049_Med_Lip_S44_4m_PTN_4 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Culture medium |
| SA218788 | LS21_049_Med_Lip_S43_4m_PTN_3 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Culture medium |
| SA218789 | LS21_049_Med_S43_4m_PTN_3 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Culture medium |
| SA218790 | LS21_049_Med_Lip_S45_4m_PTN_5 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Culture medium |
| SA218791 | LS21_049_Med_S44_4m_PTN_4 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Culture medium |
| SA218792 | LS21_049_Med_Lip_S42_4m_PTN_2 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Culture medium |
| SA218793 | LS21_049_Med_S45_4m_PTN_5 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Culture medium |
| SA218794 | LS21_049_Med_Lip_S41_4m_PTN_1 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Culture medium |
| SA218795 | LS21_049_Med_S41_4m_PTN_1 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Culture medium |
| SA218796 | LS21_049_Med_S42_4m_PTN_2 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Culture medium |
| SA218797 | LS21_049_Org_S36_4m_PTN_1 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Organoid |
| SA218798 | LS21_049_Org_S37_4m_PTN_2 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Organoid |
| SA218799 | LS21_049_Lip_Org_S37_4m_PTN_2 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Organoid |
| SA218800 | LS21_049_Org_S38_4m_PTN_3 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Organoid |
| SA218801 | LS21_049_Org_S39_4m_PTN_4 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Organoid |
| SA218802 | LS21_049_Org_S40_4m_PTN_5 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Organoid |
| SA218803 | LS21_049_Lip_Org_S38_4m_PTN_3 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Organoid |
| SA218804 | LS21_049_Lip_Org_S36_4m_PTN_1 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Organoid |
| SA218805 | LS21_049_Lip_Org_S39_4m_PTN_4 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Organoid |
| SA218806 | LS21_049_Lip_Org_S40_4m_PTN_5 | PTN; PTEN-/-; TP53-/-; NF1-/- | 4-month-old | Organoid |
