Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Patient-derived organoids (PDOs) model treatment response of metastatic gastrointestinal cancers.

ABSTRACT: We report RNAseq data from subsequent passages of five organoid cultures.

ORGANISM(S): Homo sapiens

PROVIDER: GSE108391 | GEO | 2017/12/22

SECONDARY ACCESSION(S): PRJNA427119

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Patient-derived organoids model treatment response of metastatic gastrointestinal cancers.

Project description: Not available

| S-EPMC6112415 | biostudies-literature

Patient-derived organoids (PDOs) model treatment response of metastatic gastrointestinal cancers.

Project description:Patient-derived organoids (PDOs) model treatment response of metastatic gastrointestinal cancers.

| PRJNA427119 | ENA

Patient-derived organoids (PDOs) as a novel in vitro model for neuroblastoma tumours.

Project description: Not available

| S-EPMC6802324 | biostudies-literature

DNA methylation analysis of breast cancer patient-derived xenografts and organoids

Project description:To understand if the generation of xenograft and organoid models of breast cancer alters DNA methylation, we compared the genome-wide methylation profile of matching patient tumors, patient derived xenografts, and organoid cultures derived from xenografts.

2022-01-09 | GSE186747 | GEO

Expression Analysis of Mouse Tumor and Metastatic Pancreatic Ductal Adenocarcinoma Organoids

Project description:This study used Illumina strand-specific, paired-end RNA-sequencing to examine gene expression differences between matched murine tumor- and metastasis-derived mouse pancreatic ductal adenocarcinoma (PDAC) cells grown as three-dimensional, organoid cultures. The study analyzed 16 organoid lines derived from matched primary PDAC tumors and PDAC metastases from 6 KPC (KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre) mice.

2020-06-16 | GSE142467 | GEO

Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model

Project description:Patient derived organoids (PDOs) have been established as a 3D culture model which closely recapitulates the in vivo tumor biology. However, one limitation of this culture model is the lack of tumor microenvironment which has a significant role in tumor progression and drug response. To address this, we established and molecularly characterized a novel 3D co-culture model of colorectal cancer (CRC) based on PDOs and patient matched fibroblasts. Both normal and cancer associated fibroblasts, NFs and CAFs respectively, were able to support organoid growth without addition of niche factors to the media. Additionally, co-cultures showed closer resemblance to primary patient material than organoid mono-cultures as evaluated by histology. Finally, RNA gene expression signatures of tumor cells and fibroblasts isolated from mono- or co-cultures demonstrated that co-cultures support greater cell type heterogeneity. In this proteomics dataset we compared pairs of NFs and CAFs derived from five patients. Collectively, we present a newly established human derived organoid-fibroblast model which, closely recapitulates in vivo tumor heterogeneity and involves the tumor microenvironment.

2023-03-14 | PXD032047 | Pride

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

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-to 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.

2022-02-10 | PXD023694 | Pride

TGFÎ² signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype [organoids]

Project description:The aim of this study was to determine the effects of TGFÎ² at the premalignant stage of CRC development. Organoid cultures were isolated from normal colon and from tubular adenomas. One normal colon culture was genetically engineered using the CRISPR-Cas9 system to carry the BRAFV600E mutation. Organoid cultures of three different tubular adenomas and two normal colon samples, and one BRAFV600E-mutant organoid culture received TGFÎ² or control treatment after which gene expression was analyzed by microarray (Affymetrix U133+ PM Genechip Array).

2016-06-01 | E-GEOD-79461 | biostudies-arrayexpress

Menstrual flow as a non-invasive source of endometrial organoids

Project description:Organoid cultures derived from menstrual flow faithfully replicate secretory phase endometrial glands and provide a novel, non-invasive technique for the clinical assessment of endometrial function. Paired organoid cultures derived from scratch biopsies and ensuing menstrual flow share the same transcriptome signature, responses to early pregnancy hormones, and pathological changes in cases of early-pregnancy loss. The technique opens new avenues for investigating endometrial function in cases of subfertility and gynaecological disorders.

2021-04-13 | E-MTAB-9284 | biostudies-arrayexpress

Patient-derived organoids after neoadjuvant FOLFIRINOX predict therapy resistance in pancreatic ductal adenocarcinoma

Project description:Pancreatic ductal adenocarcinoma is an extreme lethal cancer with a poor treatment response to all the current chemotherapies. We generated a library of PDAC organoid lines from resected tumors, five from treatment-naive patients and five from patients who received neoadjuvant FOLFIRINOX (eight cycles). We assessed weather residual cancer cells in the tumor lesions of the patients treated with neoadjuvant FOLFIRINOX developed resistance to the treatment. Further we perfromed transcriptome analysis to investigate: 1- weather organoids recapitualting their corresponding tumor tissue 2- To investigate any modifications in the expression of the genes inflicted by FOLFIRINOX treatment.

2021-03-23 | GSE169321 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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