Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Singel cell RNA-seq analysis of ARPKD mutation affect hepatic organoid differentiation

ABSTRACT: Singel cell RNA-seq analysis of ARPKD mutation affect hepatic organoid differentiation

PROVIDER: PRJNA647601 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Singel cell RNA-seq analysis of ARPKD mutation affect hepatic organoid differentiation

Project description:Liver fibrosis usually involve different cell types interaction. Despite its devastating consequences, there are no treatments for liver fibrosis. Genome engineering and a human hepatic organoid system was used to produce the first naïve in vitro model including several crucial components contributed for liver fibrosis. Hepatic organoids engineered to express the most common causative mutation for Autosomal Recessive Polycystic Kidney Disease (ARPKD) developed abnormal bile ducts and hepatic fibrosis in only 21 days, which are the key features of ARPKD liver pathology. Singel cell level analysis indicated that the ARPKD mutation induced bile duct proliferation through several critial pathways, and appear to be actively involved in collagen fiber generation. Therefore, abnormal cholangiocytes promotes the expansion its counterpart , which collagen-producing myofibroblasts with a markedly increased level of PDGFRB protein expression and evidence of an activated STAT3 signalling pathway.

2021-08-25 | GSE154883 | GEO

GTF2I dosage regulates neuronal differentiation and social behavior in 7q11.23 neurodevelopmental disorders Organoid SC

Project description:GTF2I dosage regulates neuronal differentiation and social behavior in 7q11.23 neurodevelopmental disorders Organoid SC

2024-06-27 | E-MTAB-13478 | biostudies-arrayexpress

The confined environment in microfluidic reveals a hidden role of self-organizing extracellular-matrix in hepatic commitment and organoid formation of hiPSCs

Project description:The specification of cell identity during human liver development is strictly controlled by extrinsic signals that restrict and define distinct cell fates. However, it is still not clear how cells, when exposed to exogenous signals, activate secretory cascades involving morphogens, growth factors and cytokines, extracellular matrix (ECM) deposition and remodeling, which are extremely relevant especially in 3D self-organizing system such as hepatic organoids. Here, we investigated how the proteins secreted by human pluripotent stem cells (hPSCs) in response to developmental exogenous signals affect the progression from endoderm to the hepatic lineage, including their competence to generate nascent hepatic organoids. By using a microfluidics-based approach coupled with SILAC-MS-based quantitative proteomic analysis we found high abundancy of ECM-associated proteins. Hepatocyte-like cells derived in microfluidics, where accumulation of cell-secreted proteins is enhanced up to 7-fold, showed organized deposition of COL1, FN, LAM and COL4, consistent with observations in human fetal liver at 8-15pcw. Further differentiation leads to a more mature hepatic transcriptomic signature and 1.5-fold higher ammonia detoxification capacity compared to conventional culture conditions. Hepatic committed cells in an early stage either derived in microfluidics and exposed to exogenous ECM stimuli show a significant higher potential for hepatic organoids formation. Nascent organoids can be rapidly expanded for several passages and further differentiated into functional hepatocytes. These results proved an additional control over the efficiency of hepatic organoid formation and differentiation for downstream applications.

2020-10-24 | GSE159926 | GEO

Integrative multi-omics analysis of intestinal organoid differentiation

Project description:Integrative multi-omics analysis of intestinal organoid differentiation

| PRJNA464352 | ENA

Highly reproducible and cost-effective one-pot organoid differentiation using a novel platform based on PF-127 triggered spheroid assembly

Project description:Using a novel platform based on the findings that Pluronic F-127 (PF-127) could trigger highly uniform spheroid assembly, we develop a one-pot organoid differentiation strategy. Using our strategy, we successfully generate cortical, nephron, hepatic, and lung organoids with improved reproducibility compared to previous methods while reducing the original costs by 80-95%. In addition, we adapt our platform to microfluidic chips allowing automated culture. We showcase that our platform can be applied to tissue-specific screening, such as drug toxicity and transfection reagents testing. And, we generate NEAT1 knockout tissue-specific organoids and show NEAT1 modulates multiple signaling pathways fine-tuning the differentiation of nephron and hepatic organoids and suppresses immune responses in cortical organoids. In summary, our strategy provides a powerful platform for advancing organoid research and studying human development and diseases.

2023-08-08 | GSE240256 | GEO

Hepatic differentiation of liver organoids

Project description:We analyzed gene expression profiles of self-organizing, multi-cellular, 3D liver organoids derived by co-culture of induced Pluripotent Stem Cell and stromal progenitors. We report the RNA-seq results of liver organoid at day0, day2, day4, day6 of co-culture. We also report RNA-seq results of constituent of the liver organoid, which are human iPSC at hepatic specification stage, human Mesenchymal stem cells derived from bone marrow, human umbilical vein endothelial cell. As controls, we also report RNS-seq results of un-differentiated human iPSC, human iPSC at definitive endoderm stage, human liver tissue, and primary cultured human hepatocytes isolated from unused donor livers.

2017-03-14 | GSE85223 | GEO

Gene expression of B cell differentiation in Organoid Cultures

Project description:To understand how different stimulation conditions impacted the maturation of B cells and formation of plasma cells in an ex vivo organoid culture, we preformed RNA-seq comparing the CD19+ B cells and CD138+ plasma cells at different time points during the organoid culture. Two stimulation conditions were used including influenza antigen alone or in combination with the TLR7 agonist R848. Finally, two B cell sources were compared to udnerstand if tissue of origin impacted organoid based B cell differentiation.

2024-08-01 | GSE268955 | GEO

Fully human umbilical cord-derived organoid for acute liver failure

Project description:We report a fully human UC-derived organoid system that integrates ECM hydrogel, MSCs and reprogrammed hepatocytes, achieving the treatment of acute hepatic failure in case of extreme failure.To explore the mechanism of our organoid in hepatic failure, we performed single cell RNA sequencing of transplanted organoids as well as the original organoid prior to transplantation, we have demonstrated that MSCs were primarily responsible for inhibiting the secretion of inflammatory-inducing cytokines and promoting the secretion of inflammation-inhibiting cytokines by recruiting immune cells migrating into organoid to triggering immune response.

2021-12-31 | GSE165944 | GEO

PLCG1 R707Q mutation is counter selected under targeted therapy in a patient with a hepatic angiosarcoma

Project description:PLCG1 R707Q mutation is counter selected under targeted therapy in a patient with a hepatic angiosarcoma

| EGAS00001001281 | EGA