Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Modelling of pancreatic cancer biology: transcriptomic signature for 3D PDX-derived organoids and primary cell line organoid development

ABSTRACT: Modelling of pancreatic cancer biology: transcriptomic signature for 3D PDX-derived organoids and primary cell line organoid development

PROVIDER: PRJNA604800 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11018030_1.fastq.gz	Fastqsanger.gz
	SRR11018030_2.fastq.gz	Fastqsanger.gz
	SRR11018031_1.fastq.gz	Fastqsanger.gz
	SRR11018031_2.fastq.gz	Fastqsanger.gz
	SRR11018032_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 128

Similar Datasets

Modelling of pancreatic cancer biology: transcriptomic signature for 3D PDX-derived organoids and primary cell line organoid development

Project description:With a five-year survival rate of 9%, pancreatic ductal adenocarcinoma (PDAC) the deadliest of all cancers. The rapid mortality makes PDAC difficult to research, and inspires a resolve to create reliable, tractable cellular models for preclinical cancer research. PDAC organoids are increasing used to model PDAC as they maintain the differentiation status, molecular and genomic signatures of the original tumour. In this paper, we present novel methodologies and experimental approaches to develop PDAC organoids from PDX tumours, and the simultaneous development of matched primary cell lines. Moreover, we also identify a method of recapitulating primary cell line cultures to organoids (CLOs). We highlight the usefulness of CLOs as PDAC organoid models, as they maintain similar transcriptomic signatures as their matched patient-derived organoids and PDXs. These models provide a manageable, expandable in vitro resource for downstream applications such as high throughput screening, functional genomics, and tumour microenvironment studies.

2020-02-05 | GSE144737 | GEO

Modelling of pancreatic cancer biology: transcriptomic signature for 3D PDX-derived organoids and primary cell line organoid development.

Project description:With a five-year survival rate of 9%, pancreatic ductal adenocarcinoma (PDAC) is the deadliest of all cancers. The rapid mortality makes PDAC difficult to research, and inspires a resolve to create reliable, tractable cellular models for preclinical cancer research. Organoids are increasingly used to model PDAC as they maintain the differentiation status, molecular and genomic signatures of the original tumour. In this paper, we present novel methodologies and experimental approaches to develop PDAC organoids from PDX tumours, and the simultaneous development of matched primary cell lines. Moreover, we also present a method of recapitulating primary cell line cultures to organoids (CLOs). We highlight the usefulness of CLOs as PDAC organoid models, as they maintain similar transcriptomic signatures as their matched patient-derived organoids and patient derived xenografts (PDX)s. These models provide a manageable, expandable in vitro resource for downstream applications such as high throughput screening, functional genomics, and tumour microenvironment studies.

| S-EPMC7026166 | biostudies-literature

Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling (passages)

Project description:Midbrain organoids are advanced in vitro cellular models for disease modelling. They have been used successfully over the past decade for Parkinson’s disease (PD) research and drug development. The three-dimensional structure and multicellular composition allow disease research under more physiological conditions than is possible with conventional 2D cellular models. However, there are concerns in the field regarding the organoid batch-to-batch variability and thus the reproducibility of the results. In this manuscript, we generate multiple independent midbrain organoid batches derived from healthy individuals or GBA-N370S mutation-carrying PD patients to evaluate the reproducibility of the GBA-N370S mutation-associated PD transcriptomic and metabolic signature as well as selected protein abundance. Our analysis shows that GBA-PD-associated phenotypes are reproducible across organoid generation batches and time points. This proves that midbrain organoids are not only suitable for PD in vitro modelling, but also represent robust and highly reproducible cellular models.

2025-07-08 | GSE287566 | GEO

Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling (timepoints)

2025-09-18 | GSE269316 | GEO

Modelling complex cardiovascular disease in mature organoid model

Project description:Cardiac maturation is an important developmental phase where there are profound biological and functional changes after birth in mammals. Herein, we use our profiling of human heart maturation in vivo to identify key drivers of maturation in our human cardiac organoid (hCO) model. In this dataset, we exemplified the applicability of our mature organoids in modelling cardiovascular disease. Pathogenesis of Desmoplakin (DSP) cardiomyopathies are driven by complex cellular interplay and changes in excitation-contraction coupling. A patient (MCHTB11), was screened against a 202 cardiac gene panel for clinically-relevant rare DNA variants (frequency < 0.04%). A homozygous 2 bp deletion was identified in the DSP gene, and recapitulated in our hCOs utilising CRISPR. In this screen, we also utilised INCB054329, a bromodomain extra-terminal inhibitor, to suppress diastolic dysfunction induced by the DSP mutant. In this dataset, we evaluate the proteomic remodelling induced by DSP-mutants (DSP) versus recovered mutants (CTRL), with and without INCB (n=3-4 for each group).

2025-04-17 | PXD054791 | Pride

Ex vivo modelling of pancreatic cancer recapitulates in vivo extracellular matrix signatures and drug responses

Project description:The ex vivo modelling of pancreatic ductal adenocarcinoma (PDAC) using patient-derived cells is a promising tool to predict treatment responses. Matrigel-based organoid and organotypic approaches are limited by their undefined molecular composition, hindering the recapitulation of the tumour’s characteristic desmoplasia, which is known to promote drug resistance. To overcome these limitations, we used self-assembling peptide amphiphiles (PAs) gelled in a minimal extracellular matrix to model the pancreatic tumour microenvironment and to establish 3D multicellular cultures of patient-derived PDAC cells, pancreatic stellate cells and macrophages. Matrisome analysis of 3D cultures demonstrated consistent ECM protein deposition, which was highly reminiscent of the corresponding primary PDAC tissues. The proteomic data obtained was also compared to the corresponding patient-derived xenografts (PDX) in nude mice and Matrigel-based cultures. Characterisation of the chemosensitivity of the cultures revealed realistic treatment responses by PDAC cells in PA hydrogels based on the responses of their corresponding PDX tumours. Histological, transcriptional and functional techniques confirmed these similarities, which were not observed in Matrigel-based cultures. These findings demonstrate the biomimetic nature of PA hydrogels, which enable cultured cells to recreate the PDAC matrisome ex vivo and to respond to chemotherapeutic agents in a predictive manner.

2021-07-06 | PXD013254 | Pride

A human bone marrow organoid for disease modelling and drug screening in blood cancers

Project description:A human bone marrow organoid for disease modelling and drug screening in blood cancers

| PRJNA806847 | ENA

Transcriptional profiling of organoid glomeruli isolated from human kidney organoids modelling congenital nephrotic syndrome

Project description:Transcriptional profiling of organoid glomeruli isolated from human kidney organoids modelling congenital nephrotic syndrome

| PRJNA846774 | ENA

Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling (timepoints)

Project description:Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling (timepoints)

| PRJNA1121199 | ENA

Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling (passages)

Project description:Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling (passages)