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MetabolomicsIntegrated Multi-omics Analysis of Human Biliary Organoids Reveals Dysregulated Metabolic and Fibro-Inflammatory Programs in Biliary Atresia
Human intrahepatic biliary organoids were established from liver tissues of children with BA (n = 11), choledochal cysts (CC, n = 5), and histologically normal controls (NC, n = 5). We performed comprehensive multi-omics profiling, including transcriptomics, proteomics, phosphoproteomics, and untarg...
2026-09-02 | MTBLS15528 | MetaboLights
MetabolomicsFirst-in-class MKK4 inhibitors enhance liver regeneration and prevent liver failure

Diminished hepatocyte regeneration is a key feature of acute and chronic liver diseases and after extended liver resections, resulting in the inability to maintain or restore a sufficient functional liver mass. Therapies to restore hepatocyte regeneration are lacking, making liver transplantation...

2024-09-23 | MTBLS9434 | MetaboLights
ProteomicsProbing the Tumour Suppressor Function of BAP1 in CRISPR-engineered Human Liver Organoids
The deubiquitinating enzyme BAP1 is a tumour suppressor, amongst others involved in cholangiocarcinoma. BAP1 has many proposed molecular targets, while its Drosophila homolog is known to deubiquitinate Histone H2AK119. Here, we mutate BAP1 by CRISPR/Cas9 in normal human liver organoids. We find that...
ORGANISM(S): Homo sapiens (Human) 
2019-05-22 | PXD013353 | Pride
Bap1 Crispr-cas9 Multiomics Human cholangiocarcinoma Human tumor modelling Human liver organoids 
GenomicsOrganoid Models of Human Liver Cancers Derived from Tumor Needle Biopsies
Hepatocellular carcinoma (HCC) is the most common primary liver cancer and the second cause of cancer-related mortality worldwide. HCC mainly arises in livers with pre-existing underlying diseases including viral hepatitis, alcoholic liver disease and nonalcoholic steatohepatitis. The multikinase in...
EGAS00001003115 | EGA
TranscriptomicsscRNAseq NOHA
To investigate the impact of hormonal modulation on neurodevelopmental processes, we performed single-cell RNA sequencing (ScRNA-seq) on neural organoids derived from two genetically validated human induced pluripotent stem cell (hiPSC) control lines (CTL08, male; CTL04, female). Organoids were chro...
ORGANISM(S): Homo sapiens 
2026-07-22 | E-MTAB-17184 | biostudies-arrayexpress
Transcriptomicsbulk RNA-seq NOHA
Bulk RNA sequencing (bulk RNA-seq) data of the Neural Organoid Hormonal Atlas (NOHA). To investigate the impact of hormonal modulation on neurodevelopmental processes, we used neural organoids derived from two genetically validated human induced pluripotent stem cell (hiPSC) control lines (CTL08, ma...
ORGANISM(S): Homo sapiens 
2026-07-22 | E-MTAB-17185 | biostudies-arrayexpress
GenomicsGene expression profiles of HYDROX-cultured human liver organoids compared to those of Matrigel-cultured human liver organoids.
Gene expression profiles of HYDROX-cultured human liver organoids compared to those of Matrigel-cultured human liver organoids.
PRJNA998921 | ENA
TranscriptomicsR-spondin 1 and noggin facilitate expansion of resident stem cells from non-damaged gallbladders.
Pioneering studies within the last few years have allowed the in vitro expansion of tissue-specific adult stem cells from a variety of endoderm-derived organs, including the stomach, small intestine and colon. Here we derived organoids from mouse gallbladder tissue (gallbladder organoids), from mous...
ORGANISM(S): Mus musculus 
2016-04-06 | E-GEOD-77461 | biostudies-arrayexpress
TranscriptomicsSingle-cell RNA sequencing of the human biliary tree
scRNA-seq of intrahepatic and extrahepatic (common bile duct and gallbladder) adult primary human cholangiocytes
ORGANISM(S): Homo sapiens 
2021-03-12 | E-MTAB-8495 | biostudies-arrayexpress
TranscriptomicsscRNA-seq of pluripotent stem cell derived human intestinal organoids, adult intestine, and human fetal endoderm derived organs
Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human definitive endoderm and intestinal organoids (HIOs) at several timepoints of in vitro growth (7, 14, and 28 days) and after in vivo growth beneath the kidney capsule of a murine host (4 and 8 wks post...
ORGANISM(S): Homo sapiens 
2021-05-21 | E-MTAB-10187 | biostudies-arrayexpress
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