Stem cell-derived organoids

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Unknown (1549)
Genomics (1131)
Transcriptomics (833)
Proteomics (63)
Other (17)
Methylation profiling (11)
Metabolomics (6)
Clinical (2)
Genomic (1)

Organisms

Homo sapiens (786)
Mus musculus (146)
Allexis (45)
Arabidopsis thaliana (45)
Callinectes sapidus (45)
Drosophila (45)
Drosophila melanogaster (45)
Ensifer adhaerens (45)
Entamoeba histolytica (45)
Escherichia coli (45)
Leishmania major strain Friedlin (45)
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Methylohalobius crimeensis 10Ki (45)
Mus musculus (45)
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Oryza sativa Indica Group (45)
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Pan troglodytes (6)
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Homo sapiens/Mus musculus xenograft (1)
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Mus (1)
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Synthetic plasmid (1)

Organisms

Homo sapiens (724)
Mus musculus (158)
Sus scrofa (7)
Canis lupus familiaris (3)
Mus (2)
Gallus gallus (2)
unidentified (1)
Macaca fascicularis (1)
Rattus norvegicus (1)

Repository

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geo (728)
biostudies-arrayexpress (188)
pride (45)
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dbGaP (1)

Tissue

Cell culture (12)
Stem cell (8)
Brain (6)
Pluripotent stem cell (5)
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Lung (2)
Multipotent stem cell (2)
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Primary cell (2)
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Early embryonic cell (1)
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Heart (1)
IMR-90 cell (1)
Intestinal epithelial cell maturation (1)
Intestinal epithelium (1)
Intestine (1)
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Kidney (1)
Microglial cell (1)
Midbrain (1)
Neural progenitor cell (1)
Neural retina (1)
Neuronal stem cell (1)
Pancreas (1)

Disease

Disease free (2)
Intestinal disease (2)
Schizophrenia (2)
Post-stasis (1)
Carcinoma (1)
Colorectal Neoplasms (1)
Alexander disease (1)
Alzheimer's disease (1)
COVID-19 (1)
Cholangiocarcinoma (1)
Colon cancer (1)
Crohn's disease (1)
Duchenne muscular dystrophy (1)
Kidney disease (1)
Leigh disease (1)
Mucinous pancreas adenocarcinoma (1)
Rectum cancer (1)

Technology Type

Mass Spectrometry (45)
Shotgun proteomics (26)
Bottom-up proteomics (9)
Data-independent acquisition (8)
Data-dependent acquisition (5)
Mass spectrometry (4)
HDMSE (3)
HiSeq X Ten (ILLUMINA) (1)
ILLUMINA, HiSeq X Ten (1)
Illumina HiSeq 2500 (1)
NMR spectroscopy assay (1)
Mass spectrometry assay (1)
Affinity purification coupled with mass spectrometry proteomics (1)
All-ion fragmentation (1)
DiaPASEF (1)
Gel-based experiment (1)
SRM/MRM (1)

Instrument Platform

Illumina NovaSeq 6000 (85)
Illumina HiSeq 2500 (26)
NextSeq 500 (19)
Illumina HiSeq 4000 (13)
N/A (6)
Illumina NovaSeq X (5)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, (4)
Fluidigm C1 (4)
Agilent 2100 Bioanalyzer (4)
NextSeq 2000 (4)
10X Genomics reagent kit (3)
Illumina HiSeq 2000 (3)
10X Chromium Nuclei Isolation Kit (2)
NextSeq 1000 (2)
NextSeq 550 (2)
Illumina NOVAseq 6000 (1)
Chromium X instrument (10x Genomics); GEM-X FX Chips (10x Genomics); Agilent TapeStation D1000; qPCR (library quantification kit for Illumina platforms) (1)
Chromium X instrument (10x Genomics); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781); Human Gene Expression Probe Set v1.0.1 (10x Genomics) (1)
Countess 3 FL Automated Cell Counter (Thermo Fisher Scientific; AMQAF2000); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781) (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Cell culture (1)
10X Chromium On-Chip Multiplex (1)
Chromium Next GEM Single Cell Multiome Reagent Bundle (1)
10X Genomics reagents (1)
IEO HPC (1)
MACS (1)
BD FACSARIA III (1)
Fludigm C1 (1)
None (1)

Publication Date

2025 (212)
2026 (178)
2023 (119)
2024 (110)
2022 (83)
2021 (81)
2020 (74)
2019 (43)
2017 (26)
2018 (22)
2015 (9)
2016 (7)
2014 (7)
2011 (5)
2013 (4)
2012 (3)
2009 (2)
2010 (1)

CHEBI ID

CHEBI:24583 (1)
CHEBI:25899 (1)
CHEBI:45744 (1)
CHEBI:84055 (1)
CHEBI:15811 (1)
CHEBI:40521 (1)
CHEBI:45826 (1)
CHEBI:18066 (1)
CHEBI:15682 (1)
CHEBI:135063 (1)
CHEBI:73028 (1)
CHEBI:15351 (1)
CHEBI:78697 (1)
CHEBI:37654 (1)
CHEBI:22211 (1)
CHEBI:30794 (1)
CHEBI:45441 (1)
CHEBI:71169 (1)
CHEBI:16831 (1)
CHEBI:16010 (1)
CHEBI:17200 (1)
CHEBI:25722 (1)
CHEBI:17822 (1)
CHEBI:15414 (1)
CHEBI:26271 (1)
CHEBI:73034 (1)
CHEBI:78320 (1)
CHEBI:17138 (1)
CHEBI:18237 (1)
CHEBI:24298 (1)

Metabolite Name

UTP (m+7) (1)
UTP (m+6) (1)
UTP (m+5) (1)
UTP (m+4) (1)
UTP (m+3) (1)
UTP (m+2) (1)
UTP (m+0) (1)
UMP (m+5) (1)
UMP (m+0) (1)
UDP-glucuronate (m+12) (1)
UDP-glucuronate (m+11) (1)
UDP-glucuronate (m+10) (1)
UDP-glucuronate (m+9) (1)
UDP-glucuronate (m+8) (1)
UDP-glucuronate (m+6) (1)
UDP-glucuronate (m+5) (1)
UDP-glucuronate (m+4) (1)
UDP-glucuronate (m+3) (1)
UDP-glucuronate (m+2) (1)
UDP-glucuronate (m+1) (1)
UDP-glucuronate (m+0) (1)
UDP-glucose (m+11) (1)
UDP-glucose (m+10) (1)
UDP-glucose (m+9) (1)
UDP-glucose (m+8) (1)
UDP-glucose (m+7) (1)
UDP-glucose (m+6) (1)
UDP-glucose (m+5) (1)
UDP-glucose (m+4) (1)
UDP-glucose (m+3) (1)

First Public Date

2025 (252)
2026 (188)
2024 (136)
2023 (122)
2022 (86)
2020 (80)
2021 (79)
2019 (52)
2017 (25)
2018 (21)
2016 (5)
2014 (5)
2015 (4)

Study status

Not yet recruiting (1)
Recruiting (1)

Study type

RNA-seq of coding RNA from single cells (70)
RNA-seq of coding RNA (51)
Transcription profiling by array (16)
Cell line - High-throughput sequencing (8)
Single nucleus RNA sequencing (5)
Methylation profiling by array (5)
RNA-seq of total RNA (5)
Cell line - Single-cell sequencing (4)
ATAC-seq (4)
Human - High-throughput sequencing (3)
ScATAC-seq (3)
Human - Single-cell sequencing (2)
Genotyping by array (2)
Comparative genomic hybridization by array (2)
Observational (2)
Null (1)
Baseline (1)
RNA-seq of non coding RNA from single cells (1)
Differential (1)
Cell line - One-color microarray (1)
High-throughput sequencing (1)
ChIP-chip by array (1)
MicroRNA profiling by high throughput sequencing (1)

Release Date

2025 (314)
2022 (238)
2024 (231)
2023 (229)
2021 (202)
2020 (139)
2019 (110)
2018 (73)
2026 (71)
2017 (55)
2015 (21)
2016 (19)
2014 (16)
2013 (8)
2011 (4)
2009 (4)
2012 (2)
2010 (1)

Lab affiliation

Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea (2)
Lab of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil (2)
1Institute of Lung Health and Immunity, Comprehensive Pneumology Center Munich with the CPC-M bioArchive, Helmholtz Center Munich, Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Germany (1)
Assistant Professor of Neurosurgery Department of Neurosurgery Houston Methodist Research Institute Weill Cornell Medical College (1)
Biomedical Research Institute, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 138648 Singapore, Singapore. Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore. (1)
CEITEC—Central European Institute of Technology, Masaryk University, Brno, Czech Republic (1)
Center for Network Systems Biology, Boston University (1)
Center for Network Systems Biology, Boston University, USA (1)
Chair in Infection and Global Health, Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, UK (1)
Chair of Proteomics and Bioanalytics, TU Munich, Germany (1)
Chair of Proteomics and Bioanalytics, Technical University of Munich Germany (1)
Children's Medical Research Insitute, The University of Sydney (1)
Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands (1)
Department of Pharmacy, Uppsala University, Box 580, SE-751 23, Uppsala, Sweden (lab head) (1)
Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, The Netherlands. (1)
Division of Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität, Planegg-Martinsried, Germany. Institute of Stem Cell Research, Helmholtz Center Munich, Planegg-Martinsried, Germany. (1)
Fondazione Pisana per la Scienza, ONLUS, San Giuliano Terme, Pisa, Italy (1)
Helmholtz Pioneer Campus, Helmholtz Zentrum München, Munich, Germany and Medical Faculty, Technical University of Munich, Munich, Germany (1)
IUSM Biochemistry and Molecular Biology, Center for Proteome Analysis, Indianapolis, IN (1)
Lab of Neuroproteomics, Institute of Biology, Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, Brazil. (1)
Laboratory of Immunoinflammation, Department of Genetics and Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Brazil (1)
Max Planck Institute of Psychiatry, Munich, Germany Biomedical Center, Molecular Biology, Ludwig-Maximilians-Universitat, Munich, Germany (1)
McGill University Department of Pharmacology and Therapeutics Centre de Recherche en Biologie Structurale (1)
Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany; 44801 Bochum, Germany (1)
Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands (1)
Molecular NeuroTherapeutics Laboratory Department of Neuroscienc Mayo Clinic Florida 4500 San Pablo Rd Jacksonville, FL 32224, USA (1)
Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands (1)
Principal Investigator „Stem Cell Metabolism“ Group Department of General Pediatrics, Neonatology, and Pediatric Cardiology University Clinic Düsseldorf (UKD), Heinrich Heine University (HHU) Moorenstraße 5, 40225 Düsseldorf, Germany Building 13.41, Level 3, Room 29 (1)
Proteomics Center, Erasmus MC (1)

Location

France (1)

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EVOLUTION 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

Mass spectrometry imaging as an emerging tool for studying metabolism in human brain organoids

Human brain organoids are emerging models to study human brain development and pathology as they recapitulate the development and characteristics of major neural cell types, and enable manipulation through an in vitro system. Over the past decade, with the advent of spatial technologies,...

2023-05-23 | MTBLS7565 | MetaboLights

Metabolic Substrate Availability Regulates Nephron Lineage Expansion in Human Kidney Organoids

Human induced pluripotent stem cell-derived kidney organoids are widely used to model nephrogenesis, but variability in basal media composition remains an underappreciated source of developmental heterogeneity. Because nephrogenesis involves rapid proliferation and differentiation, we hypothesized t...

2026-10-18 | MTBLS16048 | MetaboLights

Proteome analysis of brainstem organoids from human pluripotent stem cells

Brain organoids derived from human pluripotent stem cells recapitulate the course of human brain development. We applied proteomic analysis to human brainstem organoids which were developed by a novel method.

ORGANISM(S): Homo Sapiens (human)

2020-05-01 | PXD016807 | JPOST Repository

RNA-seq comparison of fetal lung and cultured fetal lung derived organoids with pluripotent stem cell derived lung organoids

Underdeveloped lungs are the primary cause of death in premature infants, however, little is known about stem and progenitor cell maintenance during human lung development. In this study, we have identified that FGF7, Retinoic Acid and CHIR-99021, a small molecule that inhibits GSK3 to activate Wnt ...

ORGANISM(S): Homo sapiens

2018-11-17 | E-MTAB-6023 | biostudies-arrayexpress

scRNA-seq of pluripotent stem cell derived human intestinal organoids

Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in matrigel or a non-adhesive alginate hydrogel after 28 days of in vitro growth. Additionally, we used scRNA-seq to profile HIOs derived in the presence of Neureguli...

ORGANISM(S): Homo sapiens

2021-05-21 | E-MTAB-10268 | biostudies-arrayexpress

Both wnt signaling and epidermal stem cell-derived exosomes are involved in epidermal development

Millions suffer from skin diseases. Functional epidermal stem cells are needed in skin therapy or drug screening in vitro. We obtained functional epidermal stem cells with intact stemness and cell junctions by treating them with wnt3a. Moreover, epidermal stem cell-derived exosomes were useful in ep...

ORGANISM(S): Homo Sapiens

2020-07-14 | PXD020351 |

Single-cell RNA sequencing of human pluripotent stem cell-derived RGC-enriched retinal cells generated from hESC and hiPSC retinal organoids

This study investigates the differentiation of retinal ganglion cells (RGCs) from human pluripotent stem cells (hPSCs) to optimise and characterise in-vitro RGC generation. Retinal organoids were derived from a human embryonic stem cell line (H9) and a laboratory-established human induced pluripoten...

ORGANISM(S): Homo sapiens

2026-05-30 | E-MTAB-16297 | biostudies-arrayexpress

scRNA-seq of pluripotent stem cell derived human intestinal organoids grown in an alginate matrix

Here, we used single-cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in an alginate matrix after 3, 7, and 14 days of in vitro growth. Samples were grown in minigut media supplemented with either ENR or EGF.

ORGANISM(S): Homo sapiens

2022-02-01 | E-MTAB-11338 | biostudies-arrayexpress

Single cell sequencing data of developing human intestine tissue and human and chimpanzee intestine organoids

To study the species difference in developing intestine between human and chimpanzees, we performed scMultiome profiling on developing human intestine tissues and matched intestinal epithelial only organoids (also known as enteroids), and performed scRNA-seq and scATAC-seq measurements on human and ...

ORGANISM(S): Pan troglodytes

2025-08-08 | E-MTAB-15112 | biostudies-arrayexpress

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