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MetabolomicsMetabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS
As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorecta...
2021-10-12 | MTBLS2130 | MetaboLights
MetabolomicsEVOLUTION OF THE LIPIDOME UNCOVERS EARLY CHANGES IN ADRENOLEUKODYSTROPHY HUMAN CORTICAL AND SPINAL ORGANOIDS

Lipids are critical for the structure, signaling, and metabolism of the central nervous system (CNS), yet their roles during human brain development remain underexplored due to limited tissue availability. X-linked adrenoleukodystrophy (ALD), a peroxisomal disorder caused by ABCD1 mutat...

2025-11-17 | MTBLS12973 | MetaboLights
ProteomicsProteomic analysis of induced pluripotent stem cell-derived kidney organoids
Kidney organoids were generated from a control iPSC line using a previously published protocol (https://doi.org/10.1038/nprot.2016.098). Organoids were collected at three timepoints during the protocol (day 14, 18 and 25) and prepared for proteomic analyses. The focus of the study was to define the ...
ORGANISM(S): Homo sapiens (Human) 
2021-10-13 | PXD025838 | Pride
Mass spectrometry Basement membrane Kidney organoid Enrichment Kidney Extracellular matrix 
ProteomicsHypoxic injury triggers maladaptive repair in human kidney organoids
Reduction in blood supply to the kidneys occurs to certain extent during kidney injury (AKI). Individuals who suffered AKI are at risk of developing chronic kidney disease (CKD) through a maladaptive repair process. At present, no therapies exist to prevent the AKI to CKD transition. Here, we presen...
ORGANISM(S): Homo sapiens (Human) 
2026-06-26 | PXD042882 | Pride
Acute kidney injury Metabolomics Organoids Chronic kidney disease Transcriptomics Maladaptive regeneration Proteomics Hypoxia 
ProteomicsKidney Organoids treated with TNFa at 5 ng/mL and 50ng/mL for 24h and 48h
This dataset serves as comparison for PXD029718 using a different organoid differentiation protocol – as requested by reviewers. Kidney organoids are a promising model to study kidney disease, but use is constrained by limited knowledge of their functional protein expression profile. We aimed to def...
ORGANISM(S): Homo sapiens (Human) 
2023-05-12 | PXD040812 | Pride
Human organoids kidney 
ProteomicsProteomic Profiling of Kidney Organoids in Extended Culture Conditions
We conducted a global proteomics analysis on kidney organoids at three distinct culture time points: day 22, day 33, and day 38. Our objective wasto investigate the impact of extended culture, beyond the standard differentiation endpoint of day 21, on the organoid protein expression profile.
ORGANISM(S): Homo sapiens (Human) 
2025-10-28 | PXD057360 | Pride
Proteomics Kidney organoids Extended culture Renal disease modeling 
TranscriptomicsSingle cell ATAC-seq of iPSC-derived Kidney Organoids treated with TGF-Beta 1 and GSK343 compared with vehicle treated control
This study used snATAC-seq to profile Chromatin accessibility in 26 day-old iPSC-derived kidney organoids, treated with TGFB1, the EzH2 inhibitor GSK343, a combination of both or a vehicle control for 48 hours (days 24-26) before harvesting. 2 organoids per condition were pooled and dissociated usin...
ORGANISM(S): Homo sapiens 
2023-04-30 | E-MTAB-11139 | biostudies-arrayexpress
TranscriptomicsSingle cell RNA-seq of iPSC-derived Kidney Organoids treated with TGF-Beta 1 and GSK343 compared with vehicle treated control
This study used scRNA-seq to characterise the transcriptome in 26 day-old iPSC-derived kidney organoids, treated with TGFB1, the EzH2 inhibitor GSK343, a combination of both or a vehicle control for 48 hours (days 24-26) before harvesting. 2 organoids per condition were pooled and dissociated using ...
ORGANISM(S): Homo sapiens 
2023-04-30 | E-MTAB-11138 | biostudies-arrayexpress
TranscriptomicsscRNAseq of human iPSC-derived kidney organoids transplanted in the coelomic cavity of chicken embryos compared to untransplanted controls
Human induced pluripotent stem cell-derived kidney organoids have potential for disease modelling and regenerative medicine purposes. However, they lack a functional vasculature and remain immature in in vitro culture. Here, we transplanted kidney organoids at day 7+12 of differentiation in the coel...
ORGANISM(S): Homo sapiens 
2022-08-05 | E-MTAB-11429 | biostudies-arrayexpress
TranscriptomicsscRNAseq of heterozygous HNF1B-mutant vs non-mutant kidney organoids derived from human embryonic stem cells
Human embryonic stem cell (hESC) line Man-13 was edited by CRISPR resulting in a hESC line carrying a heterozygous frameshift mutation with a premature stop codon in exon-1 of the HNF1B gene ([p.Val61Argfs*18]), functionally equivalent to a heterozygous whole-gene deletion. Kidney organoids were the...
ORGANISM(S): Homo sapiens 
2024-04-30 | E-MTAB-13500 | biostudies-arrayexpress
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