Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An extracellular matrix niche secreted by epithelial cells drives intestinal organoid formation (RNA-seq)

ABSTRACT: An extracellular matrix niche secreted by epithelial cells drives intestinal organoid formation (RNA-seq)

PROVIDER: PRJNA1244295 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR32921944.fastq.gz	Fastqsanger.gz
	SRR32921945.fastq.gz	Fastqsanger.gz
	SRR32921946.fastq.gz	Fastqsanger.gz
	SRR32921947.fastq.gz	Fastqsanger.gz
	SRR32921948.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 44

Similar Datasets

An extracellular matrix niche secreted by epithelial cells drives intestinal organoid formation (RNA-seq)

Project description:An ill-defined laminin-rich three-dimensional (3D) extracellular matrix (ECM) is typically used for the generation of organoids, but little is known about its function. Here, using tunable and chemically defined 3D hydrogels, we systematically explored the role of the ECM during murine intestinal organoid development. Our results highlight the utility of chemically defined matrices for studying ECM biology in tissue engineering and pave the way for the replacement of animal-derived matrices in organoid culture.

2025-05-21 | GSE293374 | GEO

The secreted protease Adamts18 links mammary epithelial hormone action to extracellular matrix changes and stem cell niche function

Project description:Estrogens and progesterone control mammary gland development and breast carcinogenesis via their cognate receptors expressed in a subset of cells of the luminal layer of the mammary epithelium. The extracellular matrix (ECM) including the basement membrane (BM) is important in breast physiology and tumorigenesis but how epithelial hormone receptor signaling and ECM are linked mechanistically is unclear. We identify the secreted protease Adamts18 as critical intermediary. Luminal estrogen and progesterone receptor signaling via upregulation of Wnt4 expression and ensuing canonical Wnt signaling activation in basal cells control Adamts18 expression there. The protease has an epithelial-intrinsic role in stem cell activation. We identify multiple binding partners in the interstitial ECM and BM and show that ADAMTS18 cleaves fibronectin in vitro. Its deletion results in increased fibronectin, collagen I and IV, and laminin deposition in pubertal glands. Adamts18 interacts genetically with Col18a1, which encodes a proteoglycan that is BM-specific, in stem cell regulation. Adamts18 inactivation impairs Hippo signaling and reduces Fgfr2 expression and signaling, which are vital for stem cell function. Our findings link epithelial hormone signaling to BM remodeling by Adamts18, and define the BM as an essential stem cell niche component.

2020-02-22 | GSE145680 | GEO

The secreted protease Adamts18 links mammary epithelial hormone action to extracellular matrix changes and stem cell niche function

Project description:The secreted protease Adamts18 links mammary epithelial hormone action to extracellular matrix changes and stem cell niche function

| PRJNA607942 | ENA

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

Tissue extracellular matrix hydrogels as alternative to Matrigel for culturing gastrointestinal organoid

Project description:Matrigel, a mouse tumor extracellular matrix (ECM) protein mixture, is an indispensable component of most organoid tissue culture. However, it has limited the utility of organoids for drug development and regenerative medicine due to its tumor-derived origin, batch-to22 batch variation, high cost, and safety issues. Here, we demonstrate that gastrointestinal (GI) tissue-derived ECM hydrogels are a suitable substitute for Matrigel in GI organoid culture. We found that the development and function of GI organoids grown in GI ECM hydrogels are comparable or often superior to those in Matrigel. In addition, GI ECM hydrogels enabled long-term subculture and transplantation of GI organoids by providing GI tissue-mimetic microenvironments. Tissue-specific and age-related ECM profiles of GI ECM hydrogels that affect organoid development were also elucidated through proteomic analysis. Together, our results suggest that ECM hydrogels derived from decellularized GI tissues are an effective alternative to the current gold standard, Matrigel, and produce organoids suitable for GI disease modeling, drug development, and tissue regeneration.

2022-01-31 | PXD023705 | Pride

Vascularization of cardiac organoids controls the extracellular matrix environment and regulates organoid functionality

Project description:Crosstalk between cardiac cells is critical during heart development but its role in organ maturation is still largely uncharacterised. Here, we show that endothelial cells increase the force of contraction and enhance the expression of mature sarcomeric proteins and extracellular matrix (ECM) components in human pluripotent stem cell derived cardiac organoids (hCO). Endothelial cells regulate cardiac maturation and function both directly through secretion of ECM molecules and indirectly via paracrine signaling. Laminin α5, an endothelial enriched ECM protein, was identified as a key regulator of cardiac maturation and contractility in vitro. In vivo loss-of-function studies in mice confirmed that Lama5 was required for myocardial expansion during heart development in vivo. In addition, paracrine PDGF signaling was identified as a mediator of increased ECM deposition and cardiac contractility in hCO. This study uncovers matrix regulatory functions of endothelial cells governing cardiac maturation and highlights the importance of multicellularity for organoid models.

2023-05-20 | GSE150998 | GEO

Proteome and secretome analysis of human dorsal forebrain organoids reveals a time-dependent shift in the abundance of cell adhesion and extracellular matrix proteins

Project description:Temporal dynamics of prenatal brain development are influenced by changes in the microenvironment. Particularly, extracellular proteins contribute to the dynamic niche that balances neural stem cell proliferation and differentiation. Here, we present a resource for proteome and secretome analysis of human induced pluripotent stem cell-derived dorsal forebrain organoids over the early developmental period. We used liquid chromatography-mass spectrometry to identify proteins found in whole organoid and secreted proteins at days 20, 35, and 50 of dorsal forebrain organoid differentiation. We show that the whole organoid proteome demonstrates progression in the neurodevelopmental trajectory with reduced proliferation and increased neural differentiation over time. However, secretome analysis revealed a unique signature for developmental progression. Cell adhesion molecules are enriched in the secretome of day 35 organoids, while secretome of day 50 organoids is enriched with extracellular matrix proteins, demonstrating a change in the extracellular interactions over time of organoid differentiation and maturation. We, therefore, show the relevance of secretome analysis for the thorough study of extracellular matrix-related proteins and the importance of time course study of neural organoids to understand the subtle changes that guide human neurodevelopment.

2024-05-27 | MSV000094878 | MassIVE

Human telencephalic organoid development in the presence and absence of exogenous extracellular matrix

Project description:Human telencephalic organoid development in the presence and absence of exogenous extracellular matrix

| PRJNA908783 | ENA

Vascularization of cardiac organoids controls the extracellular matrix environment and regulates organoid functionality

Project description:Vascularization of cardiac organoids controls the extracellular matrix environment and regulates organoid functionality

| PRJNA634359 | ENA

Identify the protein contents within the fluids secreted by transplanted human vascularized lung organoid

Project description:We recently established a hPSC-derived 3D organoid system to mimic the vascularization process during lung differentiation. To further mature the organoid, we embedded them into the mouse kidney capsule for three months and observed the accumulation of fluid within the growing organoids. Therefore, we aim to understand if there are any proteins related to lung function are being secreted in this case.

2025-07-06 | PXD048316 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data